BioC 3.5: CHECK report for multtest on veracruz2

Package: multtest

Version: 2.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings multtest_2.32.0.tar.gz

StartedAt: 2017-10-18 06:34:59 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:36:36 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 96.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: multtest.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings multtest_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/multtest.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.32.0’
* 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.

* installing *source* package ‘multtest’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c Rpack.c -o Rpack.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c VScount.c -o VScount.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -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  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c bootloop.c -o bootloop.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c mt.c -o mt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c pairt_sampling.c -o pairt_sampling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -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  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c random.c -o random.o
random.c:48:6: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  z1=abs(seed); /*setting the seed to z1 and initialize it*/
     ^
random.c:48:6: note: use function 'labs' instead
  z1=abs(seed); /*setting the seed to z1 and initialize it*/
     ^˜˜
     labs
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c sampling.c -o sampling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c sampling_fixed.c -o sampling_fixed.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c stat_func.c -o stat_func.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -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)

name	user	system	elapsed
EBMTP-class	0.000	0.000	0.001
EBMTP	0.460	0.019	0.486
Hsets	1.364	0.011	1.438
MTP-class	0.000	0.000	0.001
MTP	1.538	0.009	1.596
boot.null	0.113	0.001	0.117
corr.null	0.245	0.004	0.259
fwer2gfwer	3.822	0.034	3.984
get.index	0.379	0.010	0.399
meanX	0.128	0.002	0.134
mt.maxT	4.374	0.049	4.532
mt.plot	0.438	0.010	0.461
mt.rawp2adjp	0.268	0.008	0.284
mt.reject	0.267	0.007	0.278
mt.sample.teststat	0.095	0.007	0.107
mt.teststat	0.104	0.008	0.117
ss.maxT	0.000	0.000	0.001
wapply	0.001	0.000	0.002