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BioC 3.1: CHECK report for multtest on petty

This page was generated on 2015-10-09 09:32:25 -0700 (Fri, 09 Oct 2015).

Package 639/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multtest 2.24.0
Katherine S. Pollard
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/multtest
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: multtest
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings multtest_2.24.0.tar.gz
StartedAt: 2015-10-09 00:41:25 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:43:30 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 125.1 seconds
RetCode: 0
Status:  OK 
CheckDir: multtest.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings multtest_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/multtest.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.24.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘multtest’ can be installed ... [9s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘multtest/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

boot.null: no visible global function definition for ‘clusterApply’
boot.null: no visible global function definition for ‘clusterApplyLB’
EBMTP: no visible global function definition for ‘makeCluster’
EBMTP: no visible global function definition for ‘clusterEvalQ’
EBMTP: no visible global function definition for ‘stopCluster’
MTP: no visible global function definition for ‘makeCluster’
MTP: no visible global function definition for ‘clusterEvalQ’
MTP: no visible global function definition for ‘stopCluster’
EBupdate,EBMTP : .local: no visible binding for global variable ‘y’
update,MTP : .local: no visible binding for global variable ‘y’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘multtest/libs/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 entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/35s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
mt.maxT    8.117  0.066  13.432
fwer2gfwer 6.109  0.031  10.504
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/multtest.Rcheck/00check.log’
for details.


multtest.Rcheck/00install.out:

* installing *source* package ‘multtest’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c Rpack.c -o Rpack.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c VScount.c -o VScount.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c block_sampling_fixed.c -o block_sampling_fixed.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c bootloop.c -o bootloop.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c mt.c -o mt.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c pairt_sampling.c -o pairt_sampling.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c random.c -o random.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c sampling.c -o sampling.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c sampling_fixed.c -o sampling_fixed.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c stat_func.c -o stat_func.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c stat_order.c -o stat_order.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -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-3.1-bioc/meat/multtest.Rcheck/multtest/libs
** R
** data
** inst
** preparing package for lazy loading
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-class0.0010.0000.001
EBMTP0.4560.0170.780
Hsets0.4100.0070.702
MTP-class0.0010.0010.001
MTP0.6310.0071.048
boot.null0.1290.0010.202
corr.null0.0470.0040.075
fwer2gfwer 6.109 0.03110.504
get.index1.3170.0072.256
meanX0.0230.0010.042
mt.maxT 8.117 0.06613.432
mt.plot0.4880.0120.556
mt.rawp2adjp0.4220.0080.430
mt.reject0.4030.0080.410
mt.sample.teststat0.0910.0110.174
mt.teststat0.2540.0150.353
ss.maxT0.0010.0000.001
wapply0.0020.0000.003