* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/multtest.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.12.0’
* 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 whether package ‘multtest’ 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
EBMTP: warning in matrix(rep(W, p), nr = p, nc = n, byrow = TRUE):
partial argument match of 'nr' to 'nrow'
EBMTP: warning in matrix(rep(W, p), nr = p, nc = n, byrow = TRUE):
partial argument match of 'nc' to 'ncol'
EBMTP: warning in matrix(rep(W, n), nr = p, nc = n): partial argument
match of 'nr' to 'nrow'
EBMTP: warning in matrix(rep(W, n), nr = p, nc = n): partial argument
match of 'nc' to 'ncol'
EBMTP: warning in matrix(nr = 0, nc = 0): partial argument match of
'nr' to 'nrow'
EBMTP: warning in matrix(nr = 0, nc = 0): partial argument match of
'nc' to 'ncol'
EBMTP: warning in matrix(rep(marg.par, p), nr = p, nc =
length(marg.par), byrow = TRUE): partial argument match of 'nr' to
'nrow'
EBMTP: warning in matrix(rep(marg.par, p), nr = p, nc =
length(marg.par), byrow = TRUE): partial argument match of 'nc' to
'ncol'
EBMTP: warning in matrix(rep(marg.par, dim(X)[1]), nr = dim(X)[1], nc =
length(marg.par), byrow = TRUE): partial argument match of 'nr' to
'nrow'
EBMTP: warning in matrix(rep(marg.par, dim(X)[1]), nr = dim(X)[1], nc =
length(marg.par), byrow = TRUE): partial argument match of 'nc' to
'ncol'
EBMTP: warning in matrix(rep(sort.Tn, B), nr = m, nc = B): partial
argument match of 'nr' to 'nrow'
EBMTP: warning in matrix(rep(sort.Tn, B), nr = m, nc = B): partial
argument match of 'nc' to 'ncol'
EBMTP: warning in matrix(Vn, nr = clen, nc = B): partial argument match
of 'nr' to 'nrow'
EBMTP: warning in matrix(Vn, nr = clen, nc = B): partial argument match
of 'nc' to 'ncol'
EBMTP: warning in matrix(Sn, nr = clen, nc = B): partial argument match
of 'nr' to 'nrow'
EBMTP: warning in matrix(Sn, nr = clen, nc = B): partial argument match
of 'nc' to 'ncol'
EBMTP: warning in matrix(0, nr = 0, nc = 0): partial argument match of
'nr' to 'nrow'
EBMTP: warning in matrix(0, nr = 0, nc = 0): partial argument match of
'nc' to 'ncol'
Hsets: warning in matrix(rbinom(length(Tn) * B, 1, pn.out), nr =
length(Tn), nc = B): partial argument match of 'nr' to 'nrow'
Hsets: warning in matrix(rbinom(length(Tn) * B, 1, pn.out), nr =
length(Tn), nc = B): partial argument match of 'nc' to 'ncol'
IC.Cor.NA: warning in matrix(1, nr = dim(IC)[1], nc = dim(IC)[2]):
partial argument match of 'nr' to 'nrow'
IC.Cor.NA: warning in matrix(1, nr = dim(IC)[1], nc = dim(IC)[2]):
partial argument match of 'nc' to 'ncol'
IC.Cor.NA: warning in matrix(0, nr = m, nc = m): partial argument match
of 'nr' to 'nrow'
IC.Cor.NA: warning in matrix(0, nr = m, nc = m): partial argument match
of 'nc' to 'ncol'
IC.CorXW.NA: warning in matrix(0, nr = m, nc = m): partial argument
match of 'nr' to 'nrow'
IC.CorXW.NA: warning in matrix(0, nr = m, nc = m): partial argument
match of 'nc' to 'ncol'
MTP: warning in matrix(rep(W, p), nr = p, nc = n, byrow = TRUE):
partial argument match of 'nr' to 'nrow'
MTP: warning in matrix(rep(W, p), nr = p, nc = n, byrow = TRUE):
partial argument match of 'nc' to 'ncol'
MTP: warning in matrix(rep(W, n), nr = p, nc = n): partial argument
match of 'nr' to 'nrow'
MTP: warning in matrix(rep(W, n), nr = p, nc = n): partial argument
match of 'nc' to 'ncol'
MTP: warning in matrix(nr = 0, nc = 0): partial argument match of 'nr'
to 'nrow'
MTP: warning in matrix(nr = 0, nc = 0): partial argument match of 'nc'
to 'ncol'
MTP: warning in matrix(rep(marg.par, p), nr = p, nc = length(marg.par),
byrow = TRUE): partial argument match of 'nr' to 'nrow'
MTP: warning in matrix(rep(marg.par, p), nr = p, nc = length(marg.par),
byrow = TRUE): partial argument match of 'nc' to 'ncol'
MTP: warning in matrix(rep(marg.par, dim(X)[1]), nr = dim(X)[1], nc =
length(marg.par), byrow = TRUE): partial argument match of 'nr' to
'nrow'
MTP: warning in matrix(rep(marg.par, dim(X)[1]), nr = dim(X)[1], nc =
length(marg.par), byrow = TRUE): partial argument match of 'nc' to
'ncol'
boot.null: warning in matrix(nr = 0, nc = 0): partial argument match of
'nr' to 'nrow'
boot.null: warning in matrix(nr = 0, nc = 0): partial argument match of
'nc' to 'ncol'
corr.null: warning in matrix(1, nr = n, nc = 1): partial argument match
of 'nr' to 'nrow'
corr.null: warning in matrix(1, nr = n, nc = 1): partial argument match
of 'nc' to 'ncol'
corr.null: warning in matrix(1/n, nr = p, nc = n): partial argument
match of 'nr' to 'nrow'
corr.null: warning in matrix(1/n, nr = p, nc = n): partial argument
match of 'nc' to 'ncol'
corr.null: warning in matrix(0, nr = m, nc = n): partial argument match
of 'nr' to 'nrow'
corr.null: warning in matrix(0, nr = m, nc = n): partial argument match
of 'nc' to 'ncol'
corr.null: warning in matrix(1, nr = p, nc = n): partial argument match
of 'nr' to 'nrow'
corr.null: warning in matrix(1, nr = p, nc = n): partial argument match
of 'nc' to 'ncol'
corr.null: warning in matrix(1, nr = M, nc = 5): partial argument match
of 'nr' to 'nrow'
corr.null: warning in matrix(1, nr = M, nc = 5): partial argument match
of 'nc' to 'ncol'
corr.null: warning in matrix(0, nr = M, nc = N): partial argument match
of 'nr' to 'nrow'
corr.null: warning in matrix(0, nr = M, nc = N): partial argument match
of 'nc' to 'ncol'
corr.null: warning in matrix(rnorm(B * dim(IC.Cor)[1]), nr =
dim(IC.Cor)[1], nc = B): partial argument match of 'nr' to 'nrow'
corr.null: warning in matrix(rnorm(B * dim(IC.Cor)[1]), nr =
dim(IC.Cor)[1], nc = B): partial argument match of 'nc' to 'ncol'
corr.null: warning in matrix(rep(dim(X)[2] - 2, dim(IC.Cor)[1]), nr =
dim(IC.Cor)[1], nc = 1): partial argument match of 'nr' to 'nrow'
corr.null: warning in matrix(rep(dim(X)[2] - 2, dim(IC.Cor)[1]), nr =
dim(IC.Cor)[1], nc = 1): partial argument match of 'nc' to 'ncol'
corr.null: warning in matrix(rep(dim(X)[2] - dim(Z)[2],
dim(IC.Cor)[1]), nr = dim(IC.Cor)[1], nc = 1): partial argument match
of 'nr' to 'nrow'
corr.null: warning in matrix(rep(dim(X)[2] - dim(Z)[2],
dim(IC.Cor)[1]), nr = dim(IC.Cor)[1], nc = 1): partial argument match
of 'nc' to 'ncol'
corr.null: warning in matrix(rep(dim(X)[2] - dim(Z)[2] - 1,
dim(IC.Cor)[1]), nr = dim(IC.Cor)[1], nc = 1): partial argument match
of 'nr' to 'nrow'
corr.null: warning in matrix(rep(dim(X)[2] - dim(Z)[2] - 1,
dim(IC.Cor)[1]), nr = dim(IC.Cor)[1], nc = 1): partial argument match
of 'nc' to 'ncol'
corr.null: warning in matrix(rep(dim(X)[2] - 1, dim(IC.Cor)[1]), nr =
dim(IC.Cor)[1], nc = 1): partial argument match of 'nr' to 'nrow'
corr.null: warning in matrix(rep(dim(X)[2] - 1, dim(IC.Cor)[1]), nr =
dim(IC.Cor)[1], nc = 1): partial argument match of 'nc' to 'ncol'
diffs.1.N: warning in matrix(0, nr = 5, nc = length(vec1)): partial
argument match of 'nr' to 'nrow'
diffs.1.N: warning in matrix(0, nr = 5, nc = length(vec1)): partial
argument match of 'nc' to 'ncol'
fwer2fdr : get.cons: warning in matrix(nr = M, nc = nalpha): partial
argument match of 'nr' to 'nrow'
fwer2fdr : get.cons: warning in matrix(nr = M, nc = nalpha): partial
argument match of 'nc' to 'ncol'
fwer2fdr : get.restr: warning in matrix(nr = M, nc = nalpha): partial
argument match of 'nr' to 'nrow'
fwer2fdr : get.restr: warning in matrix(nr = M, nc = nalpha): partial
argument match of 'nc' to 'ncol'
fwer2fdr: warning in matrix(nr = M, nc = 2, dimnames = list(NULL,
c("conservative", "restricted"))): partial argument match of 'nr' to
'nrow'
fwer2fdr: warning in matrix(nr = M, nc = 2, dimnames = list(NULL,
c("conservative", "restricted"))): partial argument match of 'nc' to
'ncol'
fwer2fdr: warning in matrix(nr = M, nc = nalpha, dimnames = list(NULL,
paste("alpha=", alpha, sep = ""))): partial argument match of 'nr' to
'nrow'
fwer2fdr: warning in matrix(nr = M, nc = nalpha, dimnames = list(NULL,
paste("alpha=", alpha, sep = ""))): partial argument match of 'nc' to
'ncol'
print.EBMTP: warning in matrix(nr = n, nc = 4): partial argument match
of 'nr' to 'nrow'
print.EBMTP: warning in matrix(nr = n, nc = 4): partial argument match
of 'nc' to 'ncol'
print.MTP: warning in matrix(nr = n, nc = 4): partial argument match of
'nr' to 'nrow'
print.MTP: warning in matrix(nr = n, nc = 4): partial argument match of
'nc' to 'ncol'
sd.maxT: warning in matrix(nr = 0, nc = 0): partial argument match of
'nr' to 'nrow'
sd.maxT: warning in matrix(nr = 0, nc = 0): partial argument match of
'nc' to 'ncol'
sd.minP: warning in matrix(nr = 0, nc = 0): partial argument match of
'nr' to 'nrow'
sd.minP: warning in matrix(nr = 0, nc = 0): partial argument match of
'nc' to 'ncol'
ss.maxT: warning in matrix(nr = 0, nc = 0): partial argument match of
'nr' to 'nrow'
ss.maxT: warning in matrix(nr = 0, nc = 0): partial argument match of
'nc' to 'ncol'
ss.minP: warning in matrix(nr = 0, nc = 0): partial argument match of
'nr' to 'nrow'
ss.minP: warning in matrix(nr = 0, nc = 0): 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 ... WARNING
Undocumented S4 methods:
generic 'plot' and siglist 'EBMTP,ANY'
generic 'plot' and siglist 'MTP,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/multtest.Rcheck/multtest/libs/multtest.so’:
Found ‘stderr’, possibly from ‘stderr’ (C)
Objects: ‘Rpack.o’, ‘block_sampling_fixed.o’, ‘mt.o’,
‘pairt_sampling.o’, ‘pairt_sampling_fixed.o’, ‘sampling.o’,
‘sampling_fixed.o’, ‘stat_func.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
‘MTP.tex’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/multtest.Rcheck/00check.log’
for details.