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BioC 3.5: CHECK report for multtest on oaxaca

This page was generated on 2017-03-04 16:33:42 -0500 (Sat, 04 Mar 2017).

Package 840/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multtest 2.31.0
Katherine S. Pollard
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/multtest
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: multtest
Version: 2.31.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings multtest_2.31.0.tar.gz
StartedAt: 2017-03-04 06:16:11 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 06:17:45 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 93.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: multtest.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings multtest_2.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/multtest.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.31.0’
* 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 ... 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'.

EBMTP: no visible global function definition for ‘makeCluster’
EBMTP: no visible global function definition for ‘stopCluster’
EBMTP: no visible global function definition for ‘combn’
Hsets: no visible global function definition for ‘approxfun’
Hsets: no visible global function definition for ‘rbinom’
IC.Cor.NA: no visible global function definition for ‘cov2cor’
IC.CorXW.NA: no visible global function definition for ‘cov2cor’
MTP: no visible global function definition for ‘makeCluster’
MTP: no visible global function definition for ‘stopCluster’
MTP: no visible global function definition for ‘combn’
boot.null: no visible global function definition for ‘runif’
corr.Tn: no visible global function definition for ‘cov’
corr.Tn: no visible global function definition for ‘cov2cor’
corr.null: no visible global function definition for ‘cor’
corr.null: no visible global function definition for ‘cov’
corr.null: no visible global function definition for ‘cov2cor’
corr.null: no visible global function definition for ‘lm.wfit’
corr.null: no visible global function definition for ‘combn’
corr.null: no visible global function definition for ‘rnorm’
lmX : <anonymous>: no visible global function definition for ‘lm.fit’
lmX : <anonymous>: no visible global function definition for ‘lm.wfit’
lmY : <anonymous>: no visible global function definition for ‘lm.fit’
lmY : <anonymous>: no visible global function definition for ‘lm.wfit’
marg.samp: no visible global function definition for ‘rnorm’
marg.samp: no visible global function definition for ‘rt’
marg.samp: no visible global function definition for ‘rf’
mt.legend: no visible global function definition for ‘par’
mt.legend: no visible global function definition for ‘xy.coords’
mt.legend : rect2: no visible global function definition for ‘rect’
mt.legend : segments2: no visible global function definition for
  ‘segments’
mt.legend : points2: no visible global function definition for ‘points’
mt.legend : text2: no visible global function definition for ‘text’
mt.legend: no visible global function definition for ‘strwidth’
mt.legend: no visible global function definition for ‘xinch’
mt.legend: no visible global function definition for ‘yinch’
mt.legend: no visible global function definition for ‘strheight’
mt.plot: no visible global function definition for ‘matplot’
quant.trans: no visible binding for global variable ‘quantile’
sd.maxT: no visible global function definition for ‘quantile’
sd.minP: no visible global function definition for ‘quantile’
ss.maxT: no visible global function definition for ‘quantile’
ss.minP: no visible global function definition for ‘quantile’
tQuantTrans: no visible binding for global variable ‘quantile’
EBupdate,EBMTP: no visible binding for global variable ‘y’
plot,EBMTP-ANY: no visible global function definition for ‘par’
plot,EBMTP-ANY: no visible global function definition for
  ‘dev.interactive’
plot,EBMTP-ANY: no visible global function definition for ‘matplot’
plot,EBMTP-ANY: no visible global function definition for ‘title’
plot,EBMTP-ANY: no visible global function definition for ‘mtext’
plot,MTP-ANY: no visible global function definition for ‘par’
plot,MTP-ANY: no visible global function definition for
  ‘dev.interactive’
plot,MTP-ANY: no visible global function definition for ‘matplot’
plot,MTP-ANY: no visible global function definition for ‘title’
plot,MTP-ANY: no visible global function definition for ‘mtext’
plot,MTP-ANY: no visible global function definition for ‘points’
plot,MTP-ANY: no visible global function definition for ‘text’
update,MTP: no visible binding for global variable ‘y’
Undefined global functions or variables:
  approxfun combn cor cov cov2cor dev.interactive lm.fit lm.wfit
  makeCluster matplot mtext par points quantile rbinom rect rf rnorm rt
  runif segments stopCluster strheight strwidth text title xinch
  xy.coords y yinch
Consider adding
  importFrom("grDevices", "dev.interactive", "xy.coords")
  importFrom("graphics", "matplot", "mtext", "par", "points", "rect",
             "segments", "strheight", "strwidth", "text", "title",
             "xinch", "yinch")
  importFrom("stats", "approxfun", "cor", "cov", "cov2cor", "lm.fit",
             "lm.wfit", "quantile", "rbinom", "rf", "rnorm", "rt",
             "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'EBMTP,ANY,ANY,ANY'
  generic '[' and siglist 'MTP,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘MTP.pdf’, ‘MTP.tex’, ‘MTPALL.pdf’, ‘golub.R’, ‘multtest.bib’,
    ‘multtest.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/multtest.Rcheck/00check.log’
for details.


multtest.Rcheck/00install.out:

* installing *source* package ‘multtest’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c Rpack.c -o Rpack.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c VScount.c -o VScount.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c block_sampling_fixed.c -o block_sampling_fixed.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c bootloop.c -o bootloop.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c mt.c -o mt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c pairt_sampling.c -o pairt_sampling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c random.c -o random.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c sampling.c -o sampling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c sampling_fixed.c -o sampling_fixed.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c stat_func.c -o stat_func.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DUSEDOUBLE -fPIC  -Wall -mtune=core2 -g -O2  -c stat_order.c -o stat_order.o
clang -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 -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-3.5-bioc/meat/multtest.Rcheck/multtest/libs
** R
** data
** inst
** preparing package for lazy loading
** 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-class0.0010.0000.000
EBMTP0.3960.0150.411
Hsets1.4750.0051.481
MTP-class0.0000.0000.001
MTP1.4890.0041.493
boot.null0.1690.0020.170
corr.null0.2330.0020.235
fwer2gfwer3.5570.0203.580
get.index0.3800.0090.388
meanX0.1550.0020.156
mt.maxT4.0960.0264.125
mt.plot0.3770.0070.384
mt.rawp2adjp0.2740.0060.280
mt.reject0.3120.0070.319
mt.sample.teststat0.1160.0080.125
mt.teststat0.1010.0080.111
ss.maxT000
wapply0.0020.0000.002