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CHECK report for BGmix on malbec2

This page was generated on 2019-04-09 11:26:09 -0400 (Tue, 09 Apr 2019).

Package 126/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BGmix 1.43.0
Alex Lewin
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BGmix
Branch: master
Last Commit: e4824c6
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: BGmix
Version: 1.43.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BGmix.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BGmix_1.43.0.tar.gz
StartedAt: 2019-04-08 22:58:07 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:59:00 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 53.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BGmix.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BGmix.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BGmix_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BGmix.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BGmix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BGmix’ version ‘1.43.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BGmix’ can be installed ... WARNING
Found the following significant warnings:
  BGmix_main.cpp:165:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  BGmix_main.cpp:178:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  BGmix_main.cpp:179:23: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  BGmix_main.cpp:546:26: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  BGmix_main.cpp:621:26: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:192:14: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:200:14: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:870:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:883:24: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:883:65: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:893:21: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:995:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:1008:24: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:1008:65: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  updates_BGmix.cpp:1018:21: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/BGmix.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
EstimatePi0: no visible global function definition for ‘median’
EstimatePi0: no visible global function definition for ‘abline’
FDRplotTailPP: no visible global function definition for ‘plot’
SimulateFromNull: no visible global function definition for ‘rt’
SimulateFromNull: no visible global function definition for ‘rgamma’
SimulateFromNull: no visible global function definition for ‘pnorm’
TailPP: no visible global function definition for ‘par’
TailPPCalculate: no visible global function definition for ‘qnorm’
histTailPP: no visible global function definition for ‘hist’
histTailPP: no visible global function definition for ‘lines’
histTailPP: no visible global function definition for ‘density’
plotBasic: no visible global function definition for ‘par’
plotBasic: no visible global function definition for ‘plot’
plotCompare: no visible global function definition for ‘plot.default’
plotCompare: no visible global function definition for ‘abline’
plotFDR: no visible global function definition for ‘plot’
plotFDR: no visible global function definition for ‘abline’
plotFDR: no visible global function definition for ‘legend’
plotMixDensity: no visible global function definition for ‘par’
plotMixDensity: no visible global function definition for ‘hist’
plotMixDensity: no visible global function definition for ‘lines’
plotMixDensity: no visible global function definition for ‘density’
plotPredChecks: no visible global function definition for ‘hist’
plotPredChecks: no visible global function definition for ‘plot’
plotPredChecks: no visible global function definition for ‘abline’
plotTrace: no visible global function definition for ‘par’
plotTrace: no visible global function definition for ‘plot’
plotTrace: no visible global function definition for ‘dev.cur’
plotTrace: no visible global function definition for ‘X11’
Undefined global functions or variables:
  X11 abline density dev.cur hist legend lines median par plot
  plot.default pnorm qnorm rgamma rt
Consider adding
  importFrom("grDevices", "X11", "dev.cur")
  importFrom("graphics", "abline", "hist", "legend", "lines", "par",
             "plot", "plot.default")
  importFrom("stats", "density", "median", "pnorm", "qnorm", "rgamma",
             "rt")
to your NAMESPACE file.
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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 is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/BGmix/libs/BGmix.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)

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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
BGmix        6.439  0.067   6.506
FDRforTailPP 5.529  0.467   6.004
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BGmix.Rcheck/00check.log’
for details.

Installation output

BGmix.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BGmix
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BGmix’ ...
** using staged installation
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to accept ISO C99... none needed
checking for cos in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I ../boostIncl  -I/usr/local/include  -fpic  -g -O2  -Wall -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
In file included from ../boostIncl/boost/config.hpp:57:0,
                 from ../boostIncl/boost/random/linear_congruential.hpp:22,
                 from ../boostIncl/boost/random.hpp:36,
                 from rand.hh:32,
                 from updates_BGmix.h:1,
                 from BGmix_main.cpp:25:
../boostIncl/boost/random/detail/const_mod.hpp: In static member function ‘static IntType boost::random::const_mod<IntType, m>::invert_euclidian(IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_148’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/detail/const_mod.hpp:148:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(m > 0);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_152’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/detail/const_mod.hpp:152:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(boost::integer_traits<IntType>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_congruential.hpp: In constructor ‘boost::random::linear_congruential<IntType, a, c, m, val>::linear_congruential(IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_63’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_congruential.hpp:63:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp: In constructor ‘boost::random::inversive_congruential<IntType, a, b, p, val>::inversive_congruential(IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_50’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp:50:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(b >= 0);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_51’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp:51:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(p > 1);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_52’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp:52:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(a >= 1);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/shuffle_output.hpp: In member function ‘void boost::random::shuffle_output<UniformRandomNumberGenerator, k, val>::init()’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_124’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/shuffle_output.hpp:124:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/mersenne_twister.hpp: In member function ‘void boost::random::mersenne_twister<UIntType, w, n, m, r, a, u, s, b, t, c, l, val>::seed(Generator&)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_99’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/mersenne_twister.hpp:99:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<result_type>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp: In constructor ‘boost::random::subtract_with_carry<IntType, m, s, r, val>::subtract_with_carry()’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_83’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp:83:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_84’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp:84:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp: In constructor ‘boost::random::linear_feedback_shift<UIntType, w, k, q, s, val>::linear_feedback_shift(UIntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_55’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:55:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<UIntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_56’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:56:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<UIntType>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp: In constructor ‘boost::random::linear_feedback_shift<UIntType, w, k, q, s, val>::linear_feedback_shift(It&, It)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_69’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:69:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<UIntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_70’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:70:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<UIntType>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp: In member function ‘boost::random::xor_combine<URNG1, s1, URNG2, s2, val>::result_type boost::random::xor_combine<URNG1, s1, URNG2, s2, val>::operator()()’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_67’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp:67:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<typename base1_type::result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_68’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp:68:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<typename base2_type::result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_69’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp:69:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<typename base1_type::result_type>::digits >= std::numeric_limits<typename base2_type::result_type>::digits);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp: In constructor ‘boost::detail::uniform_smallint_float<UniformRandomNumberGenerator, IntType>::uniform_smallint_float(boost::detail::uniform_smallint_float<UniformRandomNumberGenerator, IntType>::base_type&, IntType, IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_121’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp:121:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_122’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp:122:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<typename base_type::result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp: In constructor ‘boost::uniform_smallint<IntType>::uniform_smallint(IntType, IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_170’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp:170:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_int.hpp: In constructor ‘boost::uniform_int<IntType>::uniform_int(IntType, IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_47’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_int.hpp:47:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/random_number_generator.hpp: In constructor ‘boost::random_number_generator<UniformRandomNumberGenerator, IntType>::random_number_generator(boost::random_number_generator<UniformRandomNumberGenerator, IntType>::base_type&)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_38’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/random_number_generator.hpp:38:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_real.hpp: In constructor ‘boost::uniform_real<RealType>::uniform_real(RealType, RealType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_41’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_real.hpp:41:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<RealType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/poisson_distribution.hpp: In constructor ‘boost::poisson_distribution<IntType, RealType>::poisson_distribution(const RealType&)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_38’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/poisson_distribution.hpp:38:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_39’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/poisson_distribution.hpp:39:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<RealType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from updates_BGmix.h:1:0,
                 from BGmix_main.cpp:25:
rand.hh: In member function ‘RealType Rand<GenType, RealType>::Normal()’:
rand.hh:368:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if(u0<.5) return y; return -y;
       ^˜
rand.hh:368:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       if(u0<.5) return y; return -y;
                           ^˜˜˜˜˜
rand.hh:375:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if(u0<.5) return y; return -y;
       ^˜
rand.hh:375:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       if(u0<.5) return y; return -y;
                           ^˜˜˜˜˜
rand.hh:382:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if(u0<.5) return y; return -y;
       ^˜
rand.hh:382:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       if(u0<.5) return y; return -y;
                           ^˜˜˜˜˜
rand.hh:389:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
     if(u0<.5) return y; return -y;
     ^˜
rand.hh:389:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
     if(u0<.5) return y; return -y;
                         ^˜˜˜˜˜
BGmix_main.cpp: In function ‘void BGmix(int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double*, double*, double*, int*, int&, double*, int*, char**, char**, char**, char**, char**)’:
BGmix_main.cpp:165:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
      if(neffects==2 & nconds==2){
         ˜˜˜˜˜˜˜˜^˜˜
BGmix_main.cpp:178:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
    if(jstar!=-1 & ncomps==3){
       ˜˜˜˜˜^˜˜˜
BGmix_main.cpp:179:23: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
      if(beta[i][jstar]<0.01 & beta[i][jstar]>-0.01) zg[i]=1;
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
BGmix_main.cpp:546:26: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
    else if(move_choice_bz==3 | move_choice_bz==4){
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
BGmix_main.cpp:621:26: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
    else if(move_choice_bz==3 | move_choice_bz==4){
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I ../boostIncl  -I/usr/local/include  -fpic  -g -O2  -Wall -DUSING_R -c rundir.cpp -o rundir.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I ../boostIncl  -I/usr/local/include  -fpic  -g -O2  -Wall -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
In file included from ../boostIncl/boost/config.hpp:57:0,
                 from ../boostIncl/boost/random/linear_congruential.hpp:22,
                 from ../boostIncl/boost/random.hpp:36,
                 from rand.hh:32,
                 from updates_BGmix.h:1,
                 from updates_BGmix.cpp:3:
../boostIncl/boost/random/detail/const_mod.hpp: In static member function ‘static IntType boost::random::const_mod<IntType, m>::invert_euclidian(IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_148’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/detail/const_mod.hpp:148:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(m > 0);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_152’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/detail/const_mod.hpp:152:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(boost::integer_traits<IntType>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_congruential.hpp: In constructor ‘boost::random::linear_congruential<IntType, a, c, m, val>::linear_congruential(IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_63’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_congruential.hpp:63:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp: In constructor ‘boost::random::inversive_congruential<IntType, a, b, p, val>::inversive_congruential(IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_50’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp:50:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(b >= 0);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_51’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp:51:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(p > 1);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_52’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/inversive_congruential.hpp:52:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(a >= 1);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/shuffle_output.hpp: In member function ‘void boost::random::shuffle_output<UniformRandomNumberGenerator, k, val>::init()’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_124’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/shuffle_output.hpp:124:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/mersenne_twister.hpp: In member function ‘void boost::random::mersenne_twister<UIntType, w, n, m, r, a, u, s, b, t, c, l, val>::seed(Generator&)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_99’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/mersenne_twister.hpp:99:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<result_type>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp: In constructor ‘boost::random::subtract_with_carry<IntType, m, s, r, val>::subtract_with_carry()’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_83’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp:83:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_84’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp:84:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp: In constructor ‘boost::random::linear_feedback_shift<UIntType, w, k, q, s, val>::linear_feedback_shift(UIntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_55’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:55:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<UIntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_56’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:56:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<UIntType>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp: In constructor ‘boost::random::linear_feedback_shift<UIntType, w, k, q, s, val>::linear_feedback_shift(It&, It)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_69’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:69:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<UIntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_70’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/linear_feedback_shift.hpp:70:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<UIntType>::is_signed);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp: In member function ‘boost::random::xor_combine<URNG1, s1, URNG2, s2, val>::result_type boost::random::xor_combine<URNG1, s1, URNG2, s2, val>::operator()()’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_67’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp:67:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<typename base1_type::result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_68’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp:68:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<typename base2_type::result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_69’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/xor_combine.hpp:69:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<typename base1_type::result_type>::digits >= std::numeric_limits<typename base2_type::result_type>::digits);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp: In constructor ‘boost::detail::uniform_smallint_float<UniformRandomNumberGenerator, IntType>::uniform_smallint_float(boost::detail::uniform_smallint_float<UniformRandomNumberGenerator, IntType>::base_type&, IntType, IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_121’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp:121:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_122’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp:122:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<typename base_type::result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp: In constructor ‘boost::uniform_smallint<IntType>::uniform_smallint(IntType, IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_170’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_smallint.hpp:170:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_int.hpp: In constructor ‘boost::uniform_int<IntType>::uniform_int(IntType, IntType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_47’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_int.hpp:47:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/random_number_generator.hpp: In constructor ‘boost::random_number_generator<UniformRandomNumberGenerator, IntType>::random_number_generator(boost::random_number_generator<UniformRandomNumberGenerator, IntType>::base_type&)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_38’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/random_number_generator.hpp:38:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_real.hpp: In constructor ‘boost::uniform_real<RealType>::uniform_real(RealType, RealType)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_41’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/uniform_real.hpp:41:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<RealType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/poisson_distribution.hpp: In constructor ‘boost::poisson_distribution<IntType, RealType>::poisson_distribution(const RealType&)’:
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_38’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/poisson_distribution.hpp:38:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef ‘boost_static_assert_typedef_39’ locally defined but not used [-Wunused-local-typedefs]
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
                     ^
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro ‘BOOST_DO_JOIN2’
 #define BOOST_DO_JOIN2( X, Y ) X##Y
                                ^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro ‘BOOST_DO_JOIN’
 #define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
                            ^˜˜˜˜˜˜˜˜˜˜˜˜
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro ‘BOOST_JOIN’
          BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
          ^˜˜˜˜˜˜˜˜˜
../boostIncl/boost/random/poisson_distribution.hpp:39:5: note: in expansion of macro ‘BOOST_STATIC_ASSERT’
     BOOST_STATIC_ASSERT(!std::numeric_limits<RealType>::is_integer);
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from updates_BGmix.h:1:0,
                 from updates_BGmix.cpp:3:
rand.hh: In member function ‘RealType Rand<GenType, RealType>::Normal()’:
rand.hh:368:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if(u0<.5) return y; return -y;
       ^˜
rand.hh:368:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       if(u0<.5) return y; return -y;
                           ^˜˜˜˜˜
rand.hh:375:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if(u0<.5) return y; return -y;
       ^˜
rand.hh:375:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       if(u0<.5) return y; return -y;
                           ^˜˜˜˜˜
rand.hh:382:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if(u0<.5) return y; return -y;
       ^˜
rand.hh:382:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       if(u0<.5) return y; return -y;
                           ^˜˜˜˜˜
rand.hh:389:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
     if(u0<.5) return y; return -y;
     ^˜
rand.hh:389:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
     if(u0<.5) return y; return -y;
                         ^˜˜˜˜˜
updates_BGmix.cpp: In function ‘void update_z_beta1_joint2(int*, double**, int*, int&, int&, double*, double&, double&, double**, double**, double**, int*, double**, double**, int&, int&, int&, int*, int&, int&, int&, Random&)’:
updates_BGmix.cpp:192:14: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   if(beta1try>0 | beta1try<-eta_down) indic = 0;
      ˜˜˜˜˜˜˜˜^˜
updates_BGmix.cpp:200:14: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   if(beta1try<0 | beta1try>eta_up) indic = 0;
      ˜˜˜˜˜˜˜˜^˜
updates_BGmix.cpp: In function ‘void predict(double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double*, double**, double*, double**, double**, double**, double**, double*, double*, int*, double**, double**, int*, double*, double&, double&, double&, double&, double&, int&, int&, int&, int&, int&, int*, int&, Random&)’:
updates_BGmix.cpp:870:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  if(move_choice_bz==1 | move_choice_bz==2){
     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp:883:24: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  else if(move_choice_bz==3 | move_choice_bz==4 |  move_choice_bz==5){
          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp:883:65: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  else if(move_choice_bz==3 | move_choice_bz==4 |  move_choice_bz==5){
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp:893:21: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
    if(move_choice_bz==3 | move_choice_bz==4) beta_jstar_pred = 0;
       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp: In function ‘void predict_t(double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double*, double*, double*, int*, double**, double**, int*, double*, double&, double&, double&, double&, double&, int&, int&, int&, int&, int&, int*, int&, Random&)’:
updates_BGmix.cpp:995:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  if(move_choice_bz==1 | move_choice_bz==2){
     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp:1008:24: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  else if(move_choice_bz==3 | move_choice_bz==4 |  move_choice_bz==5){
          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp:1008:65: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  else if(move_choice_bz==3 | move_choice_bz==4 |  move_choice_bz==5){
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp:1018:21: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
    if(move_choice_bz==3 | move_choice_bz==4) beta_jstar_pred = 0;
       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
updates_BGmix.cpp:989:5: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
 int ind;
     ^˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
rm -r ../boostIncl 
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-BGmix/00new/BGmix/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BGmix)

Tests output

Example timings

BGmix.Rcheck/BGmix-Ex.timings

nameusersystemelapsed
BGmix-package1.9420.0481.990
BGmix6.4390.0676.506
EstimatePi03.5400.1923.732
FDRforTailPP5.5290.4676.004
FDRplotTailPP2.2190.1082.336
TailPP2.1150.1722.287
calcFDR0.5410.0040.545
ccParams0.7910.0120.803
ccPred0.6560.0080.664
ccSummary0.8380.0040.842
ccTrace1.0910.0361.128
histTailPP2.3400.1362.476
plotBasic0.5140.0080.523
plotCompare0.0080.0000.008
plotFDR0.5100.0120.522
plotMixDensity1.4740.0561.530
plotPredChecks0.5480.0080.556
plotTrace0.6660.0120.694