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CHECK report for multtest on tokay2

This page was generated on 2018-10-17 08:31:46 -0400 (Wed, 17 Oct 2018).

Package 968/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multtest 2.36.0
Katherine S. Pollard
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/multtest
Branch: RELEASE_3_7
Last Commit: babb15e
Last Changed Date: 2018-04-30 10:34:54 -0400 (Mon, 30 Apr 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: multtest
Version: 2.36.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multtest.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings multtest_2.36.0.tar.gz
StartedAt: 2018-10-17 03:35:02 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:37:14 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 131.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: multtest.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multtest.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings multtest_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/multtest.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'multtest/DESCRIPTION' ... OK
* this is package 'multtest' version '2.36.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/multtest/libs/i386/multtest.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/multtest.Rcheck/00check.log'
for details.

Installation output

multtest.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/multtest_2.36.0.tar.gz && rm -rf multtest.buildbin-libdir && mkdir multtest.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multtest.buildbin-libdir multtest_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL multtest_2.36.0.zip && rm multtest_2.36.0.tar.gz multtest_2.36.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1275k  100 1275k    0     0  18.7M      0 --:--:-- --:--:-- --:--:-- 20.7M

install for i386

* installing *source* package 'multtest' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c Rpack.c -o Rpack.o
Rpack.c: In function 'get_samples_T':
Rpack.c:139:17: warning: 'sd.test' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SAMPLING_DATA sd;
                 ^
Rpack.c:143:3: warning: 'sd.fn_maxT' may be used uninitialized in this function [-Wmaybe-uninitialized]
   get_all_samples_T(V,n,T,*pna,sd.fn_maxT,sd.fn_first,sd.fn_next,(void*)extra);
   ^
Rpack.c: In function 'get_samples_P':
Rpack.c:150:17: warning: 'sd.test' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SAMPLING_DATA sd;
                 ^
Rpack.c:154:3: warning: 'sd.fn_minP' may be used uninitialized in this function [-Wmaybe-uninitialized]
   get_all_samples_P(V,n,P,*pna,sd.fn_minP,sd.fn_first,sd.fn_next,sd.fn_cmp,(void*)extra);
   ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c VScount.c -o VScount.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c block_sampling_fixed.c -o block_sampling_fixed.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c bootloop.c -o bootloop.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c mt.c -o mt.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c pairt_sampling.c -o pairt_sampling.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c random.c -o random.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c sampling.c -o sampling.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c sampling_fixed.c -o sampling_fixed.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c stat_func.c -o stat_func.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=generic -c stat_order.c -o stat_order.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o multtest.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/multtest.buildbin-libdir/multtest/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'multtest'
    finding HTML links ... done
    EBMTP-class                             html  
    EBMTP                                   html  
    Hsets                                   html  
    MTP-class                               html  
    MTP-methods                             html  
    MTP                                     html  
    boot.null                               html  
    corr.null                               html  
    fwer2gfwer                              html  
    get.index                               html  
    golub                                   html  
    meanX                                   html  
    mt.internal                             html  
    mt.maxT                                 html  
    mt.plot                                 html  
    mt.rawp2adjp                            html  
    mt.reject                               html  
    mt.sample.teststat                      html  
    mt.teststat                             html  
    ss.maxT                                 html  
    wapply                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'multtest' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c Rpack.c -o Rpack.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c VScount.c -o VScount.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c block_sampling_fixed.c -o block_sampling_fixed.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c bootloop.c -o bootloop.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c mt.c -o mt.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c pairt_sampling.c -o pairt_sampling.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c random.c -o random.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c sampling.c -o sampling.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c sampling_fixed.c -o sampling_fixed.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c stat_func.c -o stat_func.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c stat_order.c -o stat_order.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o multtest.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/multtest.buildbin-libdir/multtest/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multtest' as multtest_2.36.0.zip
* DONE (multtest)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'multtest' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

multtest.Rcheck/examples_i386/multtest-Ex.timings

nameusersystemelapsed
EBMTP-class000
EBMTP0.370.000.37
Hsets0.330.070.39
MTP-class000
MTP0.640.000.64
boot.null0.030.000.03
corr.null0.030.000.03
fwer2gfwer2.510.002.52
get.index0.250.040.29
meanX0.020.000.02
mt.maxT4.80.04.8
mt.plot0.390.000.39
mt.rawp2adjp0.340.030.37
mt.reject0.420.000.42
mt.sample.teststat0.070.030.10
mt.teststat0.090.020.11
ss.maxT000
wapply000

multtest.Rcheck/examples_x64/multtest-Ex.timings

nameusersystemelapsed
EBMTP-class000
EBMTP0.420.010.44
Hsets0.220.030.25
MTP-class000
MTP0.570.000.58
boot.null0.030.000.03
corr.null0.020.000.02
fwer2gfwer3.030.003.03
get.index0.280.020.30
meanX000
mt.maxT3.320.013.32
mt.plot0.280.020.30
mt.rawp2adjp0.260.000.27
mt.reject0.280.000.28
mt.sample.teststat0.050.020.06
mt.teststat0.050.040.09
ss.maxT000
wapply000