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BioC 3.4: CHECK report for multtest on moscato1

This page was generated on 2016-09-21 03:41:08 -0700 (Wed, 21 Sep 2016).

Package 796/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multtest 2.29.0
Katherine S. Pollard
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/multtest
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: multtest
Version: 2.29.0
Command: rm -rf multtest.buildbin-libdir multtest.Rcheck && mkdir multtest.buildbin-libdir multtest.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=multtest.buildbin-libdir multtest_2.29.0.tar.gz >multtest.Rcheck\00install.out 2>&1 && cp multtest.Rcheck\00install.out multtest-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=multtest.buildbin-libdir --install="check:multtest-install.out" --force-multiarch --no-vignettes --timings multtest_2.29.0.tar.gz
StartedAt: 2016-09-20 12:47:46 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:50:01 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 135.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: multtest.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf multtest.buildbin-libdir multtest.Rcheck && mkdir multtest.buildbin-libdir multtest.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=multtest.buildbin-libdir multtest_2.29.0.tar.gz >multtest.Rcheck\00install.out 2>&1 && cp multtest.Rcheck\00install.out multtest-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=multtest.buildbin-libdir --install="check:multtest-install.out" --force-multiarch --no-vignettes --timings multtest_2.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/multtest.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.29.0'
* 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'
center.scale: no visible binding for global variable 'var'
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'
t.effective.df: no visible global function definition for 'var'
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 var 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", "var")
  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 'D:/biocbld/bbs-3.4-bioc/meat/multtest.buildbin-libdir/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 the system RNG.
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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
mt.maxT 5.14   0.01    5.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
fwer2gfwer 4.09      0    6.88
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/multtest.Rcheck/00check.log'
for details.


multtest.Rcheck/00install.out:


install for i386

* installing *source* package 'multtest' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c VScount.c -o VScount.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c block_sampling_fixed.c -o block_sampling_fixed.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c bootloop.c -o bootloop.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c mt.c -o mt.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c pairt_sampling.c -o pairt_sampling.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c random.c -o random.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c sampling.c -o sampling.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c sampling_fixed.c -o sampling_fixed.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c stat_func.c -o stat_func.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/multtest.buildbin-libdir/multtest/libs/i386
** 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

install for x64

* installing *source* package 'multtest' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c Rpack.c -o Rpack.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c VScount.c -o VScount.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c block_sampling_fixed.c -o block_sampling_fixed.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c bootloop.c -o bootloop.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c mt.c -o mt.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c pairt_sampling.c -o pairt_sampling.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c random.c -o random.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c sampling.c -o sampling.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c sampling_fixed.c -o sampling_fixed.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c stat_func.c -o stat_func.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -DUSEDOUBLE -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/multtest.buildbin-libdir/multtest/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multtest' as multtest_2.29.0.zip
* DONE (multtest)

multtest.Rcheck/examples_i386/multtest-Ex.timings:

nameusersystemelapsed
EBMTP-class000
EBMTP0.330.000.33
Hsets0.20.00.2
MTP-class000
MTP0.330.000.33
boot.null0.060.000.06
corr.null0.000.020.01
fwer2gfwer3.110.003.11
get.index0.610.000.61
meanX0.010.000.01
mt.maxT5.140.015.15
mt.plot0.400.000.55
mt.rawp2adjp0.380.000.38
mt.reject0.340.000.34
mt.sample.teststat0.140.010.16
mt.teststat0.190.000.18
ss.maxT000
wapply000

multtest.Rcheck/examples_x64/multtest-Ex.timings:

nameusersystemelapsed
EBMTP-class000
EBMTP0.340.000.35
Hsets0.220.000.21
MTP-class000
MTP0.370.000.37
boot.null0.080.000.08
corr.null0.030.000.03
fwer2gfwer4.090.006.88
get.index0.690.000.69
meanX000
mt.maxT4.500.014.52
mt.plot0.360.000.36
mt.rawp2adjp0.330.020.35
mt.reject0.340.000.34
mt.sample.teststat0.210.000.20
mt.teststat0.210.000.22
ss.maxT000
wapply000