Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for CoGAPS on zin2

This page was generated on 2015-10-09 09:24:04 -0700 (Fri, 09 Oct 2015).

Package 198/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 2.2.0
Elana J. Fertig , Michael F. Ochs
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CoGAPS
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoGAPS
Version: 2.2.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings CoGAPS_2.2.0.tar.gz
StartedAt: 2015-10-08 23:50:01 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:51:44 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 103.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings CoGAPS_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/CoGAPS.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.2.0’
* 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 ... [43s/70s] OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
* 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/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

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.

CoGAPS.Rcheck/00install.out:

* installing *source* package ‘CoGAPS’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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]
             if (numRemoved < length) {
                              ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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]
   double lambda;
          ^
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]
   for (int m=0; m< _nFactor; ++m){
                    ^
GibbsSampler.cpp:1770:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n< _nCol; ++n){
                      ^
GibbsSampler.cpp:1783:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                       ^
GibbsSampler.cpp:1785:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:1786:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:1792:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                       ^
GibbsSampler.cpp:1794:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:1795:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:1801:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                       ^
GibbsSampler.cpp:1803:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:1804:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp:1810:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                       ^
GibbsSampler.cpp:1812:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:1813:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp:1823:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:1824:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:1829:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                       ^
GibbsSampler.cpp:1830:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                         ^
GibbsSampler.cpp:1835:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:1836:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                         ^
GibbsSampler.cpp:1841:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                       ^
GibbsSampler.cpp:1842:25: 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:1859:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:1860:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:1865:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:1866:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:1872:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:1873:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
GibbsSampler.cpp:1878:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:1879:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
GibbsSampler.cpp:1887:21: 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:1966:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                      ^
GibbsSampler.cpp:1971:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                      ^
GibbsSampler.cpp:1976:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                      ^
GibbsSampler.cpp:1981:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                      ^
GibbsSampler.cpp:1992:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:1993:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:1999:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                     ^
GibbsSampler.cpp:2000:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                     ^
GibbsSampler.cpp:2008:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:2009:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
GibbsSampler.cpp:2016:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                     ^
GibbsSampler.cpp:2017:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                     ^
GibbsSampler.cpp: In member function ‘double GibbsSampler::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 [-Wmaybe-uninitialized]
   return DelLL;
          ^
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 [-Wmaybe-uninitialized]
   return DelLL;
          ^
GibbsSampler.cpp: In member function ‘void GibbsSampler::check_atomic_matrix_consistency(char)’:
GibbsSampler.cpp:1747:49: warning: ‘total_matrix_mass’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   double diff_total_mass = fabs(total_atom_mass - total_matrix_mass);
                                                 ^
GibbsSampler.cpp:1747:49: warning: ‘total_atom_mass’ may be used uninitialized in this function [-Wmaybe-uninitialized]
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:2145:24: warning: ‘lambda’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   double mean  = (2*su - lambda)/(2*s);
                        ^
GibbsSampler.cpp:2079:23: warning: ‘iPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   unsigned int iGene, iPattern, iSample, jPattern;
                       ^
GibbsSampler.cpp:2079:16: warning: ‘iGene’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   unsigned int iGene, iPattern, iSample, jPattern;
                ^
GibbsSampler.cpp:2079:33: warning: ‘iSample’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   unsigned int iGene, iPattern, iSample, jPattern;
                                 ^
GibbsSampler.cpp: In member function ‘bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)’:
GibbsSampler.cpp:1207:3: warning: ‘bin1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1207:3: warning: ‘bin2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1255:76: warning: ‘newMass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc1,newMass1-mass1));
                                                                            ^
GibbsSampler.cpp:1255:76: warning: ‘mass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1256:76: warning: ‘newMass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1256:76: warning: ‘mass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1273:29: 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:1393:3: warning: ‘bin1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1393:3: warning: ‘bin2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1478:97: warning: ‘iSample1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1478:97: warning: ‘iSample2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1499:97: warning: ‘iGene1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1499:97: warning: ‘iGene2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1613:7: warning: ‘newMass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (newMass1 > newMass2) {
       ^
GibbsSampler.cpp:1537:28: warning: ‘newMass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  newMass1 == DOUBLE_POSINF ||
                            ^
GibbsSampler.cpp:1550:7: warning: ‘mass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (gibbsMass1 > mass2) gibbsMass1 = mass2;
       ^
GibbsSampler.cpp:1529:71: warning: ‘mass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     double plower = sub_func::pnorm(-mass1, mean, sd, DOUBLE_NEGINF, 0);
                                                                       ^
GibbsSampler.cpp:1548:65: warning: ‘sd’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       gibbsMass1 = sub_func::qnorm(u, mean, sd, DOUBLE_NEGINF, 0);
                                                                 ^
GibbsSampler.cpp:1548:65: warning: ‘mean’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1519:21: warning: ‘su’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (s == 0. && su == 0.){
                     ^
GibbsSampler.cpp:1689:29: warning: ‘delLLnew’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     update_sysChi2(delLLnew);  // update system Chi2
                             ^
GibbsSampler.cpp:1612:61: warning: ‘lambda’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       pnew = sub_func::dgamma(newMass2, 2., 1./lambda, false);
                                                             ^
GibbsSampler.cpp:1496:39: warning: ‘loc1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (_PAtomicdomain.inDomain(loc1) && _PAtomicdomain.inDomain(loc2)) 
                                       ^
GibbsSampler.cpp:1496:72: warning: ‘loc2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (_PAtomicdomain.inDomain(loc1) && _PAtomicdomain.inDomain(loc2)) 
                                                                        ^
GibbsSampler.cpp:1499:97: warning: ‘iPattern2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1499:97: warning: ‘iPattern1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                            ^
GibbsSamplerMap.cpp:96:28: 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:118:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                            ^
GibbsSamplerMap.cpp:122:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iAtom = 0; iAtom < _nRow; iAtom++){
                               ^
GibbsSamplerMap.cpp:139:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iRow = 0; iRow < _nFixedMaps; iRow++){
                            ^
GibbsSamplerMap.cpp:143:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iAtom = 0; iAtom < _nCol; iAtom++){
                               ^
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]
  bool makeNewChange; // no use. Because there is rebirth, there is nothing to check because
       ^
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]
   bool makeChange; // again, because we are birthing this just fills up list
        ^
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]
   double lambda;
          ^
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]
   for (int iRow=0; iRow < _nRow; iRow++){
                           ^
GibbsSamplerMap.cpp:1392:27: 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:202:10: 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:237:10: warning: ‘DelLL’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return DelLL;
          ^
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 [-Wmaybe-uninitialized]
  if (!makeChange){
  ^
GibbsSamplerMap.cpp:632:49: warning: ‘chCol’ may be used uninitialized in this function [-Wmaybe-uninitialized]
        update_fixed_pattern('A',newestPat,chCol);
                                                 ^
GibbsSamplerMap.cpp:639:49: warning: ‘chRow’ may be used uninitialized in this function [-Wmaybe-uninitialized]
        update_fixed_pattern('P',newestPat,chRow);
                                                 ^
GibbsSamplerMap.cpp: In member function ‘void GibbsSamplerMap::mappedExchange(char, const double* const*, const double* const*, double**, double**)’:
GibbsSamplerMap.cpp:1184:65: warning: ‘sd’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       gibbsMass1 = sub_func::qnorm(u, mean, sd, DOUBLE_NEGINF, 0);
                                                                 ^
GibbsSamplerMap.cpp:1184:65: warning: ‘mean’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSamplerMap.cpp:1155:21: warning: ‘su’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (s == 0. && su == 0.){
                     ^
GibbsSamplerMap.cpp:1273:61: warning: ‘lambda’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       pnew = sub_func::dgamma(newMass2, 2., 1./lambda, false);
                                                             ^
GibbsSamplerMap.cpp:1135:97: warning: ‘iSample2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSamplerMap.cpp:1135:97: warning: ‘iSample1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSamplerMap.cpp:1086:28: warning: ‘iPattern2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (AOrig[jGene][iPattern2] > epsilon) {
                            ^
GibbsSamplerMap.cpp:1135:97: warning: ‘iGene2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSamplerMap.cpp:1082:28: warning: ‘iPattern1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (AOrig[jGene][iPattern1] > epsilon) {
                            ^
GibbsSamplerMap.cpp:1135:97: warning: ‘iGene1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSamplerMap.cpp:1295:89: warning: ‘loc2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    makeNewCh2 = calc_new_matrix_Pattern(the_matrix_label, newPat2, loc2, newMass2-mass2);
                                                                                         ^
GibbsSamplerMap.cpp:1294:89: warning: ‘loc1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    makeNewCh1 = calc_new_matrix_Pattern(the_matrix_label, newPat1, loc1, newMass1-mass1);
                                                                                         ^
GibbsSamplerMap.cpp:1273:62: warning: ‘newMass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       pnew = sub_func::dgamma(newMass2, 2., 1./lambda, false);
                                                              ^
GibbsSamplerMap.cpp:1266:62: warning: ‘newMass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       pnew = sub_func::dgamma(newMass1, 2., 1./lambda, false);
                                                              ^
GibbsSamplerMap.cpp:1277:54: warning: ‘mass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  pold = sub_func::dgamma(mass2, 2., 1./lambda, false);
                                                      ^
GibbsSamplerMap.cpp:1275:55: warning: ‘mass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  pold = sub_func::dgamma(mass1, 2., 1./lambda,  false);
                                                       ^
GibbsSamplerMap.cpp:1206:81: warning: ‘pat2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    delLLnew+= computeDeltaLLMEMap('A',D,S,AOrig,POrig,newPat1,pat1,newPat2,pat2);
                                                                                 ^
GibbsSamplerMap.cpp:1206:81: warning: ‘pat1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSamplerMap.cpp:1056:34: warning: ‘bin2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       iSample2 = getCol('P',bin2);
                                  ^
GibbsSamplerMap.cpp:1054:34: warning: ‘bin1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       iSample1 = getCol('P',bin1);
                                  ^
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 [-Wmaybe-uninitialized]
    makeChange = calc_new_matrix_Pattern(the_matrix_label, newPat2, loc2, newMass2-mass2);
                                                                                         ^
GibbsSamplerMap.cpp:874:89: warning: ‘loc1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    makeChange = calc_new_matrix_Pattern(the_matrix_label, newPat1, loc1, newMass1-mass1);
                                                                                         ^
GibbsSamplerMap.cpp:876:77: warning: ‘newMass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                             ^
GibbsSamplerMap.cpp:873:77: warning: ‘newMass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    _new_atomicProposal.insert(pair<unsigned long long, double>(loc1,newMass1-mass1));   
                                                                             ^
GibbsSamplerMap.cpp:876:77: warning: ‘mass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                             ^
GibbsSamplerMap.cpp:873:77: warning: ‘mass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    _new_atomicProposal.insert(pair<unsigned long long, double>(loc1,newMass1-mass1));   
                                                                             ^
GibbsSamplerMap.cpp:879:95: warning: ‘pat2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    delLLnew+= computeDeltaLLMEMap(the_matrix_label, D,S,AOrig,POrig,newPat1,pat1,newPat2,pat2);
                                                                                               ^
GibbsSamplerMap.cpp:879:95: warning: ‘pat1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-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:41:21: 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:56:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:60:27: 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:87:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:91:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:92:27: 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:100:24: 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:119:23: 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:131:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                   ^
Matrix.cpp:132:25: 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:141:25: 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:149:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_row;++n) {        
                         ^
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]
         for (int n=0; n<_n_col;++n) {        
                         ^
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]
         for (int n=0; n<_n_row;++n) {        
                         ^
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]
   for (int iCol = 0; iCol < _n_col; iCol++){
                             ^
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]
   for (int iRow=0; iRow < _n_row; iRow++){
                           ^
Matrix.cpp: In member function ‘double Matrix::cal_mean() const’:
Matrix.cpp:231:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                     ^
Matrix.cpp:232:27: 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:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                     ^
Matrix.cpp:243:27: 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:305:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                   ^
Matrix.cpp:306:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {
                         ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c cogapsR.cpp -o cogapsR.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c cogapsmapR.cpp -o cogapsmapR.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c randgen.cpp -o randgen.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c sub_func.cpp -o sub_func.o
g++ -shared -L/home/biocbuild/bbs-3.1-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 randgen.o sub_func.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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
CoGAPS0.0000.0000.001
computeGeneGSProb0.0010.0000.009
gapsMapRun0.0010.0000.001
gapsRun0.0000.0040.008
plotSmoothPatterns0.0000.0000.001