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BioC 3.0: CHECK report for CoGAPS on moscato1

This page was generated on 2015-04-10 09:46:29 -0700 (Fri, 10 Apr 2015).

Package 186/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 2.0.0
Elana J. Fertig , Michael F. Ochs
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CoGAPS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CoGAPS
Version: 2.0.0
Command: rm -rf CoGAPS.buildbin-libdir CoGAPS.Rcheck && mkdir CoGAPS.buildbin-libdir CoGAPS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_2.0.0.tar.gz >CoGAPS.Rcheck\00install.out 2>&1 && cp CoGAPS.Rcheck\00install.out CoGAPS-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=CoGAPS.buildbin-libdir --install="check:CoGAPS-install.out" --force-multiarch --no-vignettes --timings CoGAPS_2.0.0.tar.gz
StartedAt: 2015-04-10 00:00:46 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:03:45 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 179.0 seconds
RetCode: 0
Status:  OK  
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CoGAPS.buildbin-libdir CoGAPS.Rcheck && mkdir CoGAPS.buildbin-libdir CoGAPS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_2.0.0.tar.gz >CoGAPS.Rcheck\00install.out 2>&1 && cp CoGAPS.Rcheck\00install.out CoGAPS-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=CoGAPS.buildbin-libdir --install="check:CoGAPS-install.out" --force-multiarch --no-vignettes --timings CoGAPS_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/CoGAPS.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoGAPS/DESCRIPTION' ... OK
* this is package 'CoGAPS' version '2.0.0'
* 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 'CoGAPS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
plotP: no visible global function definition for 'plotCI'
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... NOTE
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
* 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-3.0-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386/CoGAPS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64/CoGAPS.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [1s] OK
** running examples for arch 'x64' ... [1s] OK
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/CoGAPS.Rcheck/00check.log'
for details.

CoGAPS.Rcheck/00install.out:


install for i386

* installing *source* package 'CoGAPS' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::updateAtomicBins(double*, unsigned int, bool)':
AtomicSupport.cc:996:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GAPSNorm.cpp -o GAPSNorm.o
GAPSNorm.cpp: In static member function 'static double gaps::GAPSNorm::calChi2(const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:72:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:86:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp: In static member function 'static std::pair<double, double> gaps::GAPSNorm::calcAlphaParameters(char, unsigned int, unsigned int, unsigned int, const double* const*, const double* const*, double**, double**, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:623:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:626:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:639:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:643:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:665:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:668:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:680:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:684:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1224:10: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)':
GibbsSampler.cpp:1768:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1770:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1783:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1785:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1786:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1792:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1794:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1795:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1801:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1803:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1804:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1810:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1812:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1813:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1823:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1824:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1829:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1830:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1835:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1836:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1841:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1842:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(char*, char*, char*, char*, char*, char*, unsigned int)':
GibbsSampler.cpp:1859:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1860:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1865:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1866:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1872:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1873:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1878:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1879:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1887:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(unsigned int, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
GibbsSampler.cpp:1966:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1971:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1976:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1981:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1992:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1993:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1999:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2000:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2008:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2009:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2016:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2017:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp: In member function 'void GibbsSampler::check_atomic_matrix_consistency(char)':
GibbsSampler.cpp:1747:68: warning: 'total_matrix_mass' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1747:68: warning: 'total_atom_mass' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'double GibbsSampler::getMass(char, double, unsigned int, unsigned int, const double* const*, const double* const*, const double* const*, const double* const*, double)':
GibbsSampler.cpp:2145:38: warning: 'lambda' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:2079:23: warning: 'iPattern' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:2079:16: warning: 'iGene' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:2079:33: warning: 'iSample' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'double GibbsSampler::computeDeltaLL2(char, const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double> >)':
GibbsSampler.cpp:458:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'double GibbsSampler::computeDeltaLL(char, const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double> >)':
GibbsSampler.cpp:431:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'bool GibbsSampler::exchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:874:28: warning: 'delLLnew' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1630:10: note: 'delLLnew' was declared here
GibbsSampler.cpp:1612:61: warning: 'lambda' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1530:70: warning: 'sd' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1530:70: warning: 'mean' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1519:3: warning: 'su' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1499:97: warning: 'iGene2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1499:97: warning: 'iGene1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iSample2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iSample1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iPattern2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iPattern1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1644:83: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1643:83: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1644:83: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1643:83: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1412:32: warning: 'bin2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1410:32: warning: 'bin1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1273:51: warning: 'delLLnew' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1256:83: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1255:83: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1256:83: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1255:83: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1207:3: warning: 'bin2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1207:3: warning: 'bin1' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::init_Mapped_Matrix()':
GibbsSamplerMap.cpp:90:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:96:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::initialize_atomic_domain_map()':
GibbsSamplerMap.cpp:118:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:122:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:139:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:143:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedDeath(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:563:7: warning: variable 'makeNewChange' set but not used [-Wunused-but-set-variable]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedBirth(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:664:8: warning: variable 'makeChange' set but not used [-Wunused-but-set-variable]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedMove(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:856:10: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
GibbsSamplerMap.cpp: In member function 'bool GibbsSamplerMap::calc_new_matrix_Pattern(char, std::vector<double>&, long long unsigned int, double)':
GibbsSamplerMap.cpp:1370:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:1392:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLBDMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:202:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLMEMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:237:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedExchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:1273:61: warning: 'lambda' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1184:65: warning: 'sd' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1184:65: warning: 'mean' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1155:3: warning: 'su' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iSample2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iSample1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1042:43: warning: 'iPattern2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iGene2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1082:28: warning: 'iPattern1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iGene1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1295:89: warning: 'loc2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1294:89: warning: 'loc1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1273:62: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1266:62: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1265:5: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1265:5: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1206:80: warning: 'pat2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1206:80: warning: 'pat1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1056:34: warning: 'bin2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1054:34: warning: 'bin1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedMove(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:877:89: warning: 'loc2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:874:89: warning: 'loc1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:876:84: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:873:84: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:876:84: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:873:84: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:879:94: warning: 'pat2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:879:94: warning: 'pat1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedDeath(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:558:2: warning: 'makeChange' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:632:49: warning: 'chCol' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:639:49: warning: 'chRow' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor 'Matrix::Matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In constructor 'Matrix::Matrix(std::vector<std::vector<double> >&, char)':
Matrix.cpp:56:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:60:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In constructor 'Matrix::Matrix(const char*, char)':
Matrix.cpp:87:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:91:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:92:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In destructor 'Matrix::˜Matrix()':
Matrix.cpp:100:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::born_matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:119:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::matrix_init()':
Matrix.cpp:131:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:132:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setRow(std::vector<double>&, int)':
Matrix.cpp:141:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setCol(std::vector<double>&, int)':
Matrix.cpp:149:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setRow(const std::vector<double>&, int)':
Matrix.cpp:157:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setCol(const std::vector<double>&, int)':
Matrix.cpp:165:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::get_Row(int, std::vector<double>&) const':
Matrix.cpp:178:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::get_Col(int, std::vector<double>&) const':
Matrix.cpp:184:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'double Matrix::cal_mean() const':
Matrix.cpp:231:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:232:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'double Matrix::cal_totalsum() const':
Matrix.cpp:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:243:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::display_matrixF(std::ofstream&)':
Matrix.cpp:305:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:306:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cogapsR.cpp -o cogapsR.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cogapsmapR.cpp -o cogapsmapR.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c randgen.cpp -o randgen.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c sub_func.cpp -o sub_func.o
g++ -m32 -shared -s -static-libgcc -o CoGAPS.dll tmp.def AtomicSupport.o GAPSNorm.o GibbsSampler.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o randgen.o sub_func.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'CoGAPS' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::updateAtomicBins(double*, unsigned int, bool)':
AtomicSupport.cc:996:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GAPSNorm.cpp -o GAPSNorm.o
GAPSNorm.cpp: In static member function 'static double gaps::GAPSNorm::calChi2(const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:72:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:86:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp: In static member function 'static std::pair<double, double> gaps::GAPSNorm::calcAlphaParameters(char, unsigned int, unsigned int, unsigned int, const double* const*, const double* const*, double**, double**, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:623:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:626:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:639:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:643:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:665:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:668:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:680:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GAPSNorm.cpp:684:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1224:10: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)':
GibbsSampler.cpp:1768:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1770:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1783:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1785:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1786:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1792:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1794:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1795:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1801:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1803:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1804:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1810:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1812:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1813:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1823:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1824:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1829:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1830:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1835:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1836:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1841:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1842:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(char*, char*, char*, char*, char*, char*, unsigned int)':
GibbsSampler.cpp:1859:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1860:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1865:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1866:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1872:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1873:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1878:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1879:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1887:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(unsigned int, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
GibbsSampler.cpp:1966:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1971:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1976:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1981:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1992:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1993:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:1999:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2000:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2008:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2009:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2016:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp:2017:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSampler.cpp: In member function 'void GibbsSampler::check_atomic_matrix_consistency(char)':
GibbsSampler.cpp:1747:68: warning: 'total_matrix_mass' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1747:68: warning: 'total_atom_mass' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'double GibbsSampler::getMass(char, double, unsigned int, unsigned int, const double* const*, const double* const*, const double* const*, const double* const*, double)':
GibbsSampler.cpp:2145:38: warning: 'lambda' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:2079:23: warning: 'iPattern' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:2079:16: warning: 'iGene' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:2079:33: warning: 'iSample' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'double GibbsSampler::computeDeltaLL2(char, const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double> >)':
GibbsSampler.cpp:458:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'double GibbsSampler::computeDeltaLL(char, const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, std::vector<boost::tuples::tuple<unsigned int, unsigned int, double> >)':
GibbsSampler.cpp:431:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'bool GibbsSampler::exchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:874:28: warning: 'delLLnew' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1630:10: note: 'delLLnew' was declared here
GibbsSampler.cpp:1612:61: warning: 'lambda' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1530:70: warning: 'sd' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1530:70: warning: 'mean' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1519:3: warning: 'su' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1499:97: warning: 'iGene2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1499:97: warning: 'iGene1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iSample2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iSample1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iPattern2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1478:97: warning: 'iPattern1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1644:83: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1643:83: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1644:83: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1643:83: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1412:32: warning: 'bin2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1410:32: warning: 'bin1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1273:51: warning: 'delLLnew' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1256:83: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1255:83: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1256:83: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1255:83: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1207:3: warning: 'bin2' may be used uninitialized in this function [-Wuninitialized]
GibbsSampler.cpp:1207:3: warning: 'bin1' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::init_Mapped_Matrix()':
GibbsSamplerMap.cpp:90:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:96:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::initialize_atomic_domain_map()':
GibbsSamplerMap.cpp:118:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:122:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:139:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:143:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedDeath(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:563:7: warning: variable 'makeNewChange' set but not used [-Wunused-but-set-variable]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedBirth(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:664:8: warning: variable 'makeChange' set but not used [-Wunused-but-set-variable]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedMove(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:856:10: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
GibbsSamplerMap.cpp: In member function 'bool GibbsSamplerMap::calc_new_matrix_Pattern(char, std::vector<double>&, long long unsigned int, double)':
GibbsSamplerMap.cpp:1370:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp:1392:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLBDMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:202:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLMEMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:237:10: warning: 'DelLL' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedExchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:1273:61: warning: 'lambda' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1184:65: warning: 'sd' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1184:65: warning: 'mean' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1155:3: warning: 'su' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iSample2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iSample1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1086:28: warning: 'iPattern2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iGene2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1082:28: warning: 'iPattern1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1135:97: warning: 'iGene1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1295:89: warning: 'loc2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1294:89: warning: 'loc1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1273:62: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1266:62: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1265:5: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1265:5: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1206:80: warning: 'pat2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1206:80: warning: 'pat1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1056:34: warning: 'bin2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:1054:34: warning: 'bin1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedMove(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:877:89: warning: 'loc2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:874:89: warning: 'loc1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:876:84: warning: 'newMass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:873:84: warning: 'newMass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:876:84: warning: 'mass2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:873:84: warning: 'mass1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:879:94: warning: 'pat2' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:879:94: warning: 'pat1' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::mappedDeath(char, const double* const*, const double* const*, double**, double**)':
GibbsSamplerMap.cpp:558:2: warning: 'makeChange' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:632:49: warning: 'chCol' may be used uninitialized in this function [-Wuninitialized]
GibbsSamplerMap.cpp:639:49: warning: 'chRow' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor 'Matrix::Matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In constructor 'Matrix::Matrix(std::vector<std::vector<double> >&, char)':
Matrix.cpp:56:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:60:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In constructor 'Matrix::Matrix(const char*, char)':
Matrix.cpp:87:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:91:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:92:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In destructor 'Matrix::˜Matrix()':
Matrix.cpp:100:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::born_matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:119:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::matrix_init()':
Matrix.cpp:131:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:132:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setRow(std::vector<double>&, int)':
Matrix.cpp:141:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setCol(std::vector<double>&, int)':
Matrix.cpp:149:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setRow(const std::vector<double>&, int)':
Matrix.cpp:157:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::setCol(const std::vector<double>&, int)':
Matrix.cpp:165:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::get_Row(int, std::vector<double>&) const':
Matrix.cpp:178:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::get_Col(int, std::vector<double>&) const':
Matrix.cpp:184:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'double Matrix::cal_mean() const':
Matrix.cpp:231:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:232:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'double Matrix::cal_totalsum() const':
Matrix.cpp:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:243:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp: In member function 'void Matrix::display_matrixF(std::ofstream&)':
Matrix.cpp:305:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Matrix.cpp:306:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cogapsR.cpp -o cogapsR.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cogapsmapR.cpp -o cogapsmapR.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c randgen.cpp -o randgen.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/BH/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c sub_func.cpp -o sub_func.o
g++ -m64 -shared -s -static-libgcc -o CoGAPS.dll tmp.def AtomicSupport.o GAPSNorm.o GibbsSampler.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o randgen.o sub_func.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_2.0.0.zip
* DONE (CoGAPS)

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

nameusersystemelapsed
CoGAPS000
computeGeneGSProb000
gapsMapRun0.010.000.01
gapsRun000
plotSmoothPatterns000

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

nameusersystemelapsed
CoGAPS000
computeGeneGSProb000
gapsMapRun000
gapsRun000
plotSmoothPatterns000