- using R Under development (unstable) (2012-02-04 r58267)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘ldDesign/DESCRIPTION’ ... OK
- this is package ‘ldDesign’ version ‘2.0-0’
- 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 for executable files ... OK
- checking whether package ‘ldDesign’ 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 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
cc2x3.calc.detax.deta.general: warning in matrix(c(detax1.dR1,
detax1.dR2, detax2.dR1, detax2.dR2), nc = 2, byr = T): partial
argument match of 'nc' to 'ncol'
cc2x3.calc.detax.deta.general: warning in matrix(c(detax1.dR1,
detax1.dR2, detax2.dR1, detax2.dR2), nc = 2, byr = T): partial
argument match of 'byr' to 'byrow'
cc2x3.calc.detax.deta.general: warning in matrix(c(deta1.dR1,
deta1.dR2, deta2.dR1, deta2.dR2), nc = 2, byr = T): partial argument
match of 'nc' to 'ncol'
cc2x3.calc.detax.deta.general: warning in matrix(c(deta1.dR1,
deta1.dR2, deta2.dR1, deta2.dR2), nc = 2, byr = T): partial argument
match of 'byr' to 'byrow'
ccdesign2x2.ld.power.dominant: warning in matrix(c(p11, p12, p21, p22,
p11.new, p12.new, p21.new, p22.new), nc = 4, byr = T): partial
argument match of 'nc' to 'ncol'
ccdesign2x2.ld.power.dominant: warning in matrix(c(p11, p12, p21, p22,
p11.new, p12.new, p21.new, p22.new), nc = 4, byr = T): partial
argument match of 'byr' to 'byrow'
ccdesign2x2.ld.power.dominant: warning in matrix(c(p11, p12, p21, p22),
nc = 2, byr = T): partial argument match of 'nc' to 'ncol'
ccdesign2x2.ld.power.dominant: warning in matrix(c(p11, p12, p21, p22),
nc = 2, byr = T): partial argument match of 'byr' to 'byrow'
ccdesign2x2.ld.power.dominant: warning in matrix(c(q11, q12, q21, q22),
nc = 2, byr = T): partial argument match of 'nc' to 'ncol'
ccdesign2x2.ld.power.dominant: warning in matrix(c(q11, q12, q21, q22),
nc = 2, byr = T): partial argument match of 'byr' to 'byrow'
ccdesign2x2.ld.power.recessive: warning in matrix(c(p11, p12, p21, p22,
p11.new, p12.new, p21.new, p22.new), nc = 4, byr = T): partial
argument match of 'nc' to 'ncol'
ccdesign2x2.ld.power.recessive: warning in matrix(c(p11, p12, p21, p22,
p11.new, p12.new, p21.new, p22.new), nc = 4, byr = T): partial
argument match of 'byr' to 'byrow'
ccdesign2x2.ld.power.recessive: warning in matrix(c(p11, p12, p21,
p22), nc = 2, byr = T): partial argument match of 'nc' to 'ncol'
ccdesign2x2.ld.power.recessive: warning in matrix(c(p11, p12, p21,
p22), nc = 2, byr = T): partial argument match of 'byr' to 'byrow'
ccdesign2x2.ld.power.recessive: warning in matrix(c(q11, q12, q21,
q22), nc = 2, byr = T): partial argument match of 'nc' to 'ncol'
ccdesign2x2.ld.power.recessive: warning in matrix(c(q11, q12, q21,
q22), nc = 2, byr = T): partial argument match of 'byr' to 'byrow'
ccdesign2x3.general.ld.power: no visible binding for global variable
‘q0.soln’
ccdesign2x3.general.ld.power : calc.V: warning in matrix(c((p11 +
p12)/(p11 * p12), -1/p12, -1/p12, (p12 + p13)/(p12 * p13)), nr = 2,
nc = 2): partial argument match of 'nr' to 'nrow'
ccdesign2x3.general.ld.power : calc.V: warning in matrix(c((p11 +
p12)/(p11 * p12), -1/p12, -1/p12, (p12 + p13)/(p12 * p13)), nr = 2,
nc = 2): partial argument match of 'nc' to 'ncol'
ccdesign2x3.general.ld.power : calc.V: warning in matrix(c((p21 +
p22)/(p21 * p22), -1/p22, -1/p22, (p22 + p23)/(p22 * p23)), nr = 2,
nc = 2): partial argument match of 'nr' to 'nrow'
ccdesign2x3.general.ld.power : calc.V: warning in matrix(c((p21 +
p22)/(p21 * p22), -1/p22, -1/p22, (p22 + p23)/(p22 * p23)), nr = 2,
nc = 2): partial argument match of 'nc' to 'ncol'
ccdesign2x3.ld.power: warning in matrix(c(p11, p12, p13, p21, p22,
p23), nr = 2, byr = T): partial argument match of 'nr' to 'nrow'
ccdesign2x3.ld.power: warning in matrix(c(p11, p12, p13, p21, p22,
p23), nr = 2, byr = T): partial argument match of 'byr' to 'byrow'
ccdesign2x3.ld.power: warning in matrix(c(q11, q12, q13, q21, q22,
q23), nr = 2, byr = T): partial argument match of 'nr' to 'nrow'
ccdesign2x3.ld.power: warning in matrix(c(q11, q12, q13, q21, q22,
q23), nr = 2, byr = T): partial argument match of 'byr' to 'byrow'
ld.sim: warning in matrix(aperm(array(sapply(res, c), dim =
c(sim.chunk, 4, ncalls)), c(1, 3, 2)), nc = 4): partial argument
match of 'nc' to 'ncol'
ld.sim1: warning in matrix(rbinom(n0 * nreps, size = 1, prob = Q), nc =
nreps): partial argument match of 'nc' to 'ncol'
ld.sim1: warning in matrix(rbinom(n0 * nreps, size = 1, prob = R), nc =
nreps): partial argument match of 'nc' to 'ncol'
ld.sim1: warning in matrix(ifelse(qval1 == 1, ifelse(qval2 == 1, d, h),
ifelse(qval2 == 1, h, -d)), nc = nreps): partial argument match of
'nc' to 'ncol'
ld.sim1: warning in matrix(ifelse(r1 == 1, ifelse(r2 == 1, d, h),
ifelse(r2 == 1, h, -d)), nc = nreps): partial argument match of 'nc'
to 'ncol'
ld.sim1: warning in matrix(c(p^2 * Q^2, 2 * p^2 * Q * (1 - Q), p^2 * (1
- Q)^2, 2 * p * (1 - p) * Q * R, 2 * p * (1 - p) * (Q + R - 2 * Q *
R), 2 * p * (1 - p) * (1 - Q) * (1 - R), (1 - p)^2 * R^2, 2 * (1 -
p)^2 * R * (1 - R), (1 - p)^2 * (1 - R)^2), nc = 3, byrow = TRUE):
partial argument match of 'nc' to 'ncol'
ld.sim1: warning in matrix(rep(f1.q, 3), nc = 3, byrow = TRUE): partial
argument match of 'nc' to 'ncol'
ld.sim1: warning in matrix(mq0, nc = nreps): partial argument match of
'nc' to 'ncol'
ld.sim1: warning in matrix(mq1, nc = nreps): partial argument match of
'nc' to 'ncol'
ld.sim1: warning in matrix(yq, nc = nreps): partial argument match of
'nc' to 'ncol'
ld.sim1: warning in matrix(err, nc = nreps): partial argument match of
'nc' to 'ncol'
ld.sim1: warning in matrix(nr = nreps, nc = 4): partial argument match
of 'nr' to 'nrow'
ld.sim1: warning in matrix(nr = nreps, nc = 4): partial argument match
of 'nc' to 'ncol'
luo.ld.power : method1.calc.ems: warning in matrix(rep(c(q^2, 2 * q *
(1 - q), (1 - q)^2), 3), nc = 3, byrow = TRUE): partial argument
match of 'nc' to 'ncol'
luo.ld.power: warning in matrix(c(p^2 * Q^2, 2 * p^2 * Q * (1 - Q), p^2
* (1 - Q)^2, 2 * p * (1 - p) * Q * R, 2 * p * (1 - p) * (Q + R - 2 *
Q * R), 2 * p * (1 - p) * (1 - Q) * (1 - R), (1 - p)^2 * R^2, 2 * (1
- p)^2 * R * (1 - R), (1 - p)^2 * (1 - R)^2), nr = 3, nc = 3, byrow =
TRUE): partial argument match of 'nr' to 'nrow'
luo.ld.power: warning in matrix(c(p^2 * Q^2, 2 * p^2 * Q * (1 - Q), p^2
* (1 - Q)^2, 2 * p * (1 - p) * Q * R, 2 * p * (1 - p) * (Q + R - 2 *
Q * R), 2 * p * (1 - p) * (1 - Q) * (1 - R), (1 - p)^2 * R^2, 2 * (1
- p)^2 * R * (1 - R), (1 - p)^2 * (1 - R)^2), nr = 3, nc = 3, byrow =
TRUE): partial argument match of 'nc' to 'ncol'
luo.ld.power: warning in matrix(NA, nr = 3, nc = 3): partial argument
match of 'nr' to 'nrow'
luo.ld.power: warning in matrix(NA, nr = 3, nc = 3): partial argument
match of 'nc' to 'ncol'
- 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 sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
The following files should probably not be installed:
‘Makefile’, ‘ldDesign.tex’
The following directories should probably not be installed:
‘auto’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
- checking examples ... [7s/7s] OK
- checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘nlme’
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [1s/1s] WARNING
Errors in running code in vignettes:
when running code in ‘ldDesign.Rnw’
...
[1] 24245
> calc.Balpha.ABF(alpha = 5e-08, n = 1e+05, a = 1)
[1] 8971
> library(nlme)
When sourcing ‘ldDesign.R’:
Error: there is no package called ‘nlme’
Execution halted
- checking re-building of vignette PDFs ... [2s/2s] OK
- checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/ldDesign.Rcheck/00check.log’
for details.