Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 369/565HostnameOS / ArchBUILDCHECKBUILD BIN
multtest 2.13.0
Katherine S. Pollard
Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/multtest
Last Changed Rev: 64680 / Revision: 66885
Last Changed Date: 2012-03-30 15:15:56 -0700 (Fri, 30 Mar 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: multtest
Version: 2.13.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch multtest_2.13.0.tar.gz
StartedAt: 2012-06-21 01:57:12 -0700 (Thu, 21 Jun 2012)
EndedAt: 2012-06-21 01:59:04 -0700 (Thu, 21 Jun 2012)
EllapsedTime: 111.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: multtest.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/multtest.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'multtest/DESCRIPTION' ... OK
* this is package 'multtest' version '2.13.0'
* 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 '/Users/biocbuild/bbs-2.11-bioc/meat/multtest.Rcheck/multtest/libs/i386/multtest.so':
  Found '___stderrp', 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'MTPALL.pdf' from 274Kb to 168Kb
     compacted 'multtest.pdf' from 1660Kb to 409Kb
  consider running tools::compactPDF() on these files
* 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 4 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/multtest.Rcheck/00check.log'
for details.

multtest.Rcheck/00install.out:

* installing *source* package 'multtest' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c Rpack.c -o Rpack.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c VScount.c -o VScount.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c bootloop.c -o bootloop.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c mt.c -o mt.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c pairt_sampling.c -o pairt_sampling.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c random.c -o random.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c sampling.c -o sampling.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c sampling_fixed.c -o sampling_fixed.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c stat_func.c -o stat_func.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -g -O2 -Wall -pedantic  -c stat_order.c -o stat_order.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/multtest.Rcheck/multtest/libs/i386
** 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
EBMTP0.3940.0130.456
Hsets0.3890.0100.487
MTP-class0.0000.0010.000
MTP0.5750.0050.678
boot.null0.1400.0010.164
corr.null0.0520.0080.064
fwer2gfwer5.4860.0246.528
get.index1.4740.0111.554
meanX0.0150.0010.015
mt.maxT10.041 0.07211.298
mt.plot0.6100.0100.628
mt.rawp2adjp0.5430.0070.558
mt.reject0.5290.0080.539
mt.sample.teststat0.1130.0120.127
mt.teststat0.3830.0420.428
ss.maxT0.0000.0000.001
wapply0.0010.0000.001