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BioC 3.2: CHECK report for CoGAPS on zin1

This page was generated on 2016-04-23 10:11:28 -0700 (Sat, 23 Apr 2016).

Package 208/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 2.4.0
Elana J. Fertig
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CoGAPS
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoGAPS
Version: 2.4.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CoGAPS_2.4.0.tar.gz
StartedAt: 2016-04-22 23:26:54 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:28:17 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 83.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CoGAPS_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CoGAPS.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoGAPS’ can be installed ... [61s/65s] OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] 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

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.


CoGAPS.Rcheck/00install.out:

* installing *source* package ‘CoGAPS’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function ‘void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, const char*)’:
AtomicSupport.cc:143:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin)
                   ^
AtomicSupport.cc: In member function ‘void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, std::vector<std::vector<double> >)’:
AtomicSupport.cc:218:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin)
                   ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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]
         for (int m=0; m < nRow; ++m){
                           ^
GAPSNorm.cpp:86:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m=0; m < nRow; ++m)
                           ^
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]
    for (int jSample = 0; jSample < nCol; jSample++) {
                                    ^
GAPSNorm.cpp:626:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                        ^
GAPSNorm.cpp:639:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jSample = 0; jSample < nCol; jSample++) {
                                    ^
GAPSNorm.cpp:643:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                        ^
GAPSNorm.cpp:665:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jGene = 0; jGene < nRow; jGene++) {
                                ^
GAPSNorm.cpp:668:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                        ^
GAPSNorm.cpp:680:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jGene = 0; jGene < nRow; jGene++) {
                                ^
GAPSNorm.cpp:684:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                        ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c GibbsSampler.cpp -o GibbsSampler.o
GibbsSampler.cpp: In member function ‘std::vector<std::vector<std::vector<double> > > GibbsSampler::getNormedMatrices()’:
GibbsSampler.cpp:511:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m< _nFactor; ++m){
                    ^
GibbsSampler.cpp:513:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n< _nCol; ++n){
                      ^
GibbsSampler.cpp:521:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:522:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:527:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:528:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp: In member function ‘std::vector<std::vector<double> > GibbsSampler::createSampleAMat(std::map<long long unsigned int, double>)’:
GibbsSampler.cpp:560:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nRow; i++){
                      ^
GibbsSampler.cpp: In member function ‘std::vector<std::vector<double> > GibbsSampler::createSamplePMat(std::map<long long unsigned int, double>)’:
GibbsSampler.cpp:580:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nFactor; i++){
                      ^
GibbsSampler.cpp: In member function ‘bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)’:
GibbsSampler.cpp:1489:10: warning: variable ‘lambda’ set but not used [-Wunused-but-set-variable]
   double lambda;
          ^
GibbsSampler.cpp: In member function ‘void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)’:
GibbsSampler.cpp:2036:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m< _nFactor; ++m){
                    ^
GibbsSampler.cpp:2038:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n< _nCol; ++n){
                      ^
GibbsSampler.cpp:2051:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                       ^
GibbsSampler.cpp:2053:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:2054:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:2060:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                       ^
GibbsSampler.cpp:2062:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:2063:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:2069:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                       ^
GibbsSampler.cpp:2071:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:2072:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp:2078:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                       ^
GibbsSampler.cpp:2080:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:2081:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp:2091:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:2092:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:2097:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:2098:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:2103:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:2104:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp:2109:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:2110:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp: In member function ‘void GibbsSampler::compute_statistics(char*, char*, char*, char*, char*, char*, unsigned int)’:
GibbsSampler.cpp:2127:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:2128:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:2133:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:2134:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:2140:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:2141:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
GibbsSampler.cpp:2146:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:2147:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
GibbsSampler.cpp:2155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m)
                     ^
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:2234:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                      ^
GibbsSampler.cpp:2239:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                      ^
GibbsSampler.cpp:2244:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                      ^
GibbsSampler.cpp:2249:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                      ^
GibbsSampler.cpp:2260:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:2261:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:2267:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:2268:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:2276:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:2277:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
GibbsSampler.cpp:2284:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:2285:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
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:2406:24: warning: ‘lambda’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   double mean  = (2*su - lambda)/(2*s);
                        ^
GibbsSampler.cpp: In member function ‘bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)’:
GibbsSampler.cpp:1472:3: warning: ‘bin1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1472:3: warning: ‘bin2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1520:76: warning: ‘newMass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc1,newMass1-mass1));
                                                                            ^
GibbsSampler.cpp:1520:76: warning: ‘mass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1521:76: warning: ‘newMass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1521:76: warning: ‘mass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1538:29: warning: ‘delLLnew’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     tmp = priorLL + delLLnew*_annealingTemperature;
                             ^
GibbsSampler.cpp: In member function ‘bool GibbsSampler::exchange(char, const double* const*, const double* const*, double**, double**)’:
GibbsSampler.cpp:1658:3: warning: ‘bin1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1658:3: warning: ‘bin2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1743:97: warning: ‘iSample1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1743:97: warning: ‘iSample2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: ‘iGene1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1764:97: warning: ‘iGene2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1909:76: warning: ‘newMass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1802:28: warning: ‘newMass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  newMass1 == DOUBLE_POSINF ||
                            ^
GibbsSampler.cpp:1815:7: warning: ‘mass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (gibbsMass1 > mass2) gibbsMass1 = mass2;
       ^
GibbsSampler.cpp:1794:71: warning: ‘mass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     double plower = sub_func::pnorm(-mass1, mean, sd, DOUBLE_NEGINF, 0);
                                                                       ^
GibbsSampler.cpp:1813:65: warning: ‘sd’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       gibbsMass1 = sub_func::qnorm(u, mean, sd, DOUBLE_NEGINF, 0);
                                                                 ^
GibbsSampler.cpp:1813:65: warning: ‘mean’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1784:21: warning: ‘su’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (s == 0. && su == 0.){
                     ^
GibbsSampler.cpp:1954:29: warning: ‘delLLnew’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     update_sysChi2(delLLnew);  // update system Chi2
                             ^
GibbsSampler.cpp:1877:61: warning: ‘lambda’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       pnew = sub_func::dgamma(newMass2, 2., 1./lambda, false);
                                                             ^
GibbsSampler.cpp:1761:39: warning: ‘loc1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (_PAtomicdomain.inDomain(loc1) && _PAtomicdomain.inDomain(loc2)) 
                                       ^
GibbsSampler.cpp:1761:72: warning: ‘loc2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (_PAtomicdomain.inDomain(loc1) && _PAtomicdomain.inDomain(loc2)) 
                                                                        ^
GibbsSampler.cpp:1764:97: warning: ‘iPattern2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1764:97: warning: ‘iPattern1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In constructor ‘GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, const string&, const string&, const string&, std::vector<std::vector<double> >&, char)’:
GibbsSamplerMap.cpp:48:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < parameters.size(); i++){
                                       ^
GibbsSamplerMap.cpp:52:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                                           ^
GibbsSamplerMap.cpp:55:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                                           ^
GibbsSamplerMap.cpp: In constructor ‘GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const string&, std::vector<std::vector<double> >&, char)’:
GibbsSamplerMap.cpp:79:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < parameters.size(); i++){
                                       ^
GibbsSamplerMap.cpp:83:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                                           ^
GibbsSamplerMap.cpp:86:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                                           ^
GibbsSamplerMap.cpp: In member function ‘void GibbsSamplerMap::init_Mapped_Matrix()’:
GibbsSamplerMap.cpp:111:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                            ^
GibbsSamplerMap.cpp:117:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iRow = 0; iRow < _nFixedMaps; iRow++){
                            ^
GibbsSamplerMap.cpp: In member function ‘void GibbsSamplerMap::initialize_atomic_domain_map()’:
GibbsSamplerMap.cpp:140:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                            ^
GibbsSamplerMap.cpp:144:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iAtom = 0; iAtom < _nRow; iAtom++){
                               ^
GibbsSamplerMap.cpp:161:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iRow = 0; iRow < _nFixedMaps; iRow++){
                            ^
GibbsSamplerMap.cpp:167:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iAtom = 0; iAtom < _nCol; iAtom++){
                                ^
GibbsSamplerMap.cpp: In member function ‘std::vector<std::vector<double> > GibbsSamplerMap::createSampleAMatMap(std::map<long long unsigned int, double>)’:
GibbsSamplerMap.cpp:520:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nRow; i++){
                      ^
GibbsSamplerMap.cpp:540:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iRow=0; iRow < _nRow; iRow++){
                            ^
GibbsSamplerMap.cpp: In member function ‘std::vector<std::vector<double> > GibbsSamplerMap::createSamplePMatMap(std::map<long long unsigned int, double>)’:
GibbsSamplerMap.cpp:556:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nFactor; i++){
                      ^
GibbsSamplerMap.cpp:577:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iCol=0; iCol < _nCol; iCol++){
                            ^
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:219:10: warning: ‘DelLL’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return DelLL;
          ^
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:254:10: warning: ‘DelLL’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return DelLL;
          ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor ‘Matrix::Matrix(unsigned int, unsigned int, char, double)’:
Matrix.cpp:44:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _n_row ; ++m){
                     ^
Matrix.cpp: In constructor ‘Matrix::Matrix(std::vector<std::vector<double> >&, char)’:
Matrix.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:62:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:63:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In constructor ‘Matrix::Matrix(const char*, char)’:
Matrix.cpp:90:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:94:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:95:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In destructor ‘Matrix::˜Matrix()’:
Matrix.cpp:103:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0 ; m < _n_row ; ++m)
                        ^
Matrix.cpp: In member function ‘void Matrix::born_matrix(unsigned int, unsigned int, char, double)’:
Matrix.cpp:122:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp: In member function ‘void Matrix::matrix_init()’:
Matrix.cpp:134:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                   ^
Matrix.cpp:135:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {        
                         ^
Matrix.cpp: In member function ‘void Matrix::setRow(std::vector<double>, int)’:
Matrix.cpp:160:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {        
                         ^
Matrix.cpp: In member function ‘void Matrix::setCol(std::vector<double>, int)’:
Matrix.cpp:168:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_row;++n) {        
                         ^
Matrix.cpp: In member function ‘std::vector<double> Matrix::get_Row(int)’:
Matrix.cpp:182:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iCol = 0; iCol < _n_col; iCol++){
                             ^
Matrix.cpp: In member function ‘std::vector<double> Matrix::get_Col(int)’:
Matrix.cpp:190:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iRow=0; iRow < _n_row; iRow++){
                           ^
Matrix.cpp: In member function ‘double Matrix::cal_mean() const’:
Matrix.cpp:238:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                     ^
Matrix.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col;++n) {
                           ^
Matrix.cpp: In member function ‘double Matrix::cal_totalsum() const’:
Matrix.cpp:249:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                     ^
Matrix.cpp:250:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col;++n) {
                           ^
Matrix.cpp: In member function ‘void Matrix::display_matrixF(std::ofstream&)’:
Matrix.cpp:313:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                   ^
Matrix.cpp:314:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {
                         ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c cogapsR.cpp -o cogapsR.o
cogapsR.cpp: In function ‘Rcpp::List cogaps(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)’:
cogapsR.cpp:442:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                             ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c cogapsmapR.cpp -o cogapsmapR.o
cogapsmapR.cpp: In function ‘Rcpp::List cogapsMap(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)’:
cogapsmapR.cpp:401:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                             ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c cogapsmaptestR.cpp -o cogapsmaptestR.o
cogapsmaptestR.cpp: In function ‘Rcpp::List cogapsMapTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)’:
cogapsmaptestR.cpp:481:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                             ^
cogapsmaptestR.cpp:598:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iEquil=0; iEquil < nEquil; iEquil++){
                               ^
cogapsmaptestR.cpp:607:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iSample=0; iSample < nSample; iSample++){
                                 ^
cogapsmaptestR.cpp:699:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapsmaptestR.cpp:715:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
cogapsmaptestR.cpp:731:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapsmaptestR.cpp:747:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
cogapsmaptestR.cpp:776:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapsmaptestR.cpp:791:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
cogapsmaptestR.cpp:806:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapsmaptestR.cpp:821:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c cogapstestR.cpp -o cogapstestR.o
cogapstestR.cpp: In function ‘Rcpp::List cogapsTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)’:
cogapstestR.cpp:509:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                             ^
cogapstestR.cpp:634:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iEquil=0; iEquil < nEquil; iEquil++){
                              ^
cogapstestR.cpp:643:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iSample=0; iSample < nSample; iSample++){
                                ^
cogapstestR.cpp:733:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapstestR.cpp:749:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
cogapstestR.cpp:765:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapstestR.cpp:781:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
cogapstestR.cpp:809:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapstestR.cpp:824:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
cogapstestR.cpp:839:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                     ^
cogapstestR.cpp:854:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                     ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c randgen.cpp -o randgen.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c sub_func.cpp -o sub_func.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o CoGAPS.so AtomicSupport.o GAPSNorm.o GibbsSampler.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o cogapsmaptestR.o cogapstestR.o randgen.o sub_func.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/CoGAPS.Rcheck/CoGAPS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CoGAPS)

CoGAPS.Rcheck/CoGAPS-Ex.timings:

nameusersystemelapsed
CoGAPS0.0010.0000.001
computeGeneGSProb0.0020.0000.002
gapsInterPattern0.0010.0000.000
gapsIntraPattern0.0010.0000.001
gapsMapRun0.0010.0000.001
gapsMapTestRun0.0020.0000.001
gapsRun0.0010.0000.000
gapsTestRun0.0010.0000.001
plotSmoothPatterns0.0010.0000.001