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Package 361/554HostnameOS / ArchBUILDCHECKBUILD BIN
multtest 2.12.0
Katherine S. Pollard
Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/multtest
Last Changed Rev: 64678 / Revision: 64719
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
puck5 Linux (Ubuntu 12.04) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: multtest
Version: 2.12.0
Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings multtest_2.12.0.tar.gz
StartedAt: 2012-04-01 02:19:43 -0700 (Sun, 01 Apr 2012)
EndedAt: 2012-04-01 02:20:41 -0700 (Sun, 01 Apr 2012)
EllapsedTime: 57.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: multtest.Rcheck
Warnings: 1

Command output

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/multtest.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* 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/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/meat/multtest.Rcheck/00check.log'
for details.

multtest.Rcheck/00install.out:

* installing *source* package 'multtest' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c Rpack.c -o Rpack.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c VScount.c -o VScount.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c bootloop.c -o bootloop.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c mt.c -o mt.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c pairt_sampling.c -o pairt_sampling.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c random.c -o random.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c sampling.c -o sampling.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c sampling_fixed.c -o sampling_fixed.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c stat_func.c -o stat_func.o
stat_func.c: In function 'read_infile':
stat_func.c:703:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
stat_func.c:705:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
stat_func.c:710:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
stat_func.c:714:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c stat_order.c -o stat_order.o
gcc -std=gnu99 -shared -L/usr/local/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/multtest.Rcheck/multtest/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'as.list' from package 'base' in package 'multtest'
Creating a generic function for 'update' from package 'stats' in package 'multtest'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

* DONE (multtest)

multtest.Rcheck/multtest-Ex.timings:

nameusersystemelapsed
EBMTP-class000
EBMTP0.2120.0000.213
Hsets0.2560.0040.259
MTP-class0.0000.0000.001
MTP0.4040.0040.409
boot.null0.0800.0000.082
corr.null0.0320.0040.030
fwer2gfwer3.2920.0083.307
get.index0.8040.0080.812
meanX0.0080.0000.007
mt.maxT3.8800.0043.887
mt.plot0.3440.0120.367
mt.rawp2adjp0.3280.0000.334
mt.reject0.3000.0200.332
mt.sample.teststat0.0600.0040.072
mt.teststat0.1960.0040.209
ss.maxT000
wapply0.0000.0000.001