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BioC 3.5: CHECK report for flipflop on oaxaca

This page was generated on 2017-03-04 16:46:25 -0500 (Sat, 04 Mar 2017).

Package 428/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flipflop 1.13.0
Elsa Bernard
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flipflop
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: flipflop
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flipflop_1.13.0.tar.gz
StartedAt: 2017-03-04 02:46:19 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 02:48:44 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 145.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flipflop.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flipflop_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flipflop.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.13.0’
* 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 ‘flipflop’ 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
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -stdlib=libstdc++
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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 ... 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/flipflop.Rcheck/00check.log’
for details.

flipflop.Rcheck/00install.out:

* installing *source* package ‘flipflop’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c FileSplitter.cpp -o FileSplitter.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_flipflop.c -o R_init_flipflop.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c align.cpp -o align.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c auxiliaryio.cpp -o auxiliaryio.o
In file included from auxiliaryio.cpp:6:
In file included from ./auxiliaryio.h:11:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
auxiliaryio.cpp:904:9: warning: unused variable 'id' [-Wunused-variable]
    int id;
        ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c bedio.cpp -o bedio.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c common.cpp -o common.o
In file included from common.cpp:5:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c cvganalysis.cpp -o cvganalysis.o
In file included from cvganalysis.cpp:2:
In file included from ./cvganalysis.h:9:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
cvganalysis.cpp:156:12: warning: unused variable 'prevjump' [-Wunused-variable]
      bool prevjump=false;
           ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c ffProcesssam.cpp -o ffProcesssam.o
In file included from ffProcesssam.cpp:3:
In file included from ./samio.h:10:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c instanceio.cpp -o instanceio.o
In file included from instanceio.cpp:2:
In file included from ./instanceio.h:7:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
instanceio.cpp:125:9: warning: unused variable 'currenttypeorder' [-Wunused-variable]
    int currenttypeorder=-1;
        ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c parseopt.cpp -o parseopt.o
In file included from parseopt.cpp:1:
In file included from ./parseopt.h:9:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c rangeset.cpp -o rangeset.o
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
  long t=0;
       ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
readgroup.cpp:408:31: warning: unused variable 'vr_end' [-Wunused-variable]
  vector<ReadGroup>::iterator vr_end = vr.end();
                              ^
readgroup.cpp:1274:7: warning: unused variable 'npos' [-Wunused-variable]
  int npos=0,nneg=0;
      ^
readgroup.cpp:1274:14: warning: unused variable 'nneg' [-Wunused-variable]
  int npos=0,nneg=0;
             ^
readgroup.cpp:1273:7: warning: unused variable 'r' [-Wunused-variable]
  int r=0;
      ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c samio.cpp -o samio.o
In file included from samio.cpp:12:
In file included from ./samio.h:10:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
samio.cpp:149:7: warning: unused variable 'rangecounter' [-Wunused-variable]
  int rangecounter=1;
      ^
samio.cpp:153:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
  int currentreadlen=0;
      ^
samio.cpp:145:11: warning: unused variable 'dp2' [-Wunused-variable]
  range_t dp2=dp;
          ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c samples.cpp -o samples.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c spams.cpp -o spams.o
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3111:17: warning: unused variable 'pr' [-Wunused-variable]
      const int pr=_pr_node[i];
                ^
spams/prox/project.h:3450:12: warning: 10 enumeration values not handled in switch: 'FLOW_LINEAR', 'FLOW_SQUARE', 'FLOW_SQUARE_POS'... [-Wswitch]
   switch (loss) {
           ^
spams/prox/project.h:3709:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
   switch (loss) {
           ^
spams/prox/project.h:3738:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
   switch (loss) {
           ^
spams/prox/project.h:3761:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
   switch (loss) {
           ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:83:15: warning: 9 enumeration values not handled in switch: 'SQUARE', 'SQUARE_MISSING', 'LOG'... [-Wswitch]
      switch (loss) {
              ^
spams/prox/fista.h:101:15: warning: 36 enumeration values not handled in switch: 'L0', 'L1', 'RIDGE'... [-Wswitch]
      switch (regul) {
              ^
spams/prox/fista.h:3588:24: warning: unused variable 'duality' [-Wunused-variable]
            const bool duality = losses[0]->is_fenchel() && regularizers[0]->is_fenchel();
                       ^
spams/prox/fista.h:3635:24: warning: unused variable 'duality' [-Wunused-variable]
            const bool duality = losses[0]->is_fenchel() && regularizers[0]->is_fenchel();
                       ^
spams/prox/fista.h:3788:30: warning: unused variable 'duality' [-Wunused-variable]
                  const bool duality = loss->is_fenchel() && regularizer->is_fenchel();
                             ^
spams/prox/fista.h:3963:21: warning: 6 enumeration values not handled in switch: 'FLOW_LINEAR', 'FLOW_SQUARE_POS', 'FLOW_SQUARE_POS_WEIGHTS'... [-Wswitch]
            switch (loss) {
                    ^
spams/prox/fista.h:3693:24: warning: 7 enumeration values not handled in switch: 'SQUARE_MISSING', 'LOG', 'LOGWEIGHT'... [-Wswitch]
               switch (param.loss) {
                       ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3720:27: warning: 4 enumeration values not handled in switch: 'MULTILOG', 'CUR', 'HINGE'... [-Wswitch]
                  switch (param.loss) {
                          ^
spams/prox/fista.h:3752:27: warning: 8 enumeration values not handled in switch: 'SQUARE', 'SQUARE_MISSING', 'LOG'... [-Wswitch]
                  switch (param.loss) {
                          ^
spams/prox/fista.h:3772:24: warning: enumeration values 'MULTILOG', 'HINGE', and 'INCORRECT_LOSS' not handled in switch [-Wswitch]
               switch (param.loss) {
                       ^
spams/prox/fista.h:3396:18: warning: 33 enumeration values not handled in switch: 'L0', 'L1', 'RIDGE'... [-Wswitch]
         switch (param.regul) {
                 ^
spams/prox/fista.h:3692:32: note: in instantiation of function template specialization 'FISTA::setRegularizerADMM<double>' requested here
               regularizers[i]=setRegularizerADMM(param,graph_st,tree_st);
                               ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3426:18: warning: 11 enumeration values not handled in switch: 'L1L2', 'L1LINF', 'L1L2_L1'... [-Wswitch]
         switch (param.regul) {
                 ^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
                  regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
                                  ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3738:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
   switch (loss) {
           ^
spams/prox/project.h:3991:40: note: in instantiation of member function 'DoubleMinCostFlow<double>::eval_flow_derivative_arc' requested here
            const T reduced_cost=this->eval_flow_derivative_arc(node,j)-target;
                                       ^
spams/prox/project.h:3804:14: note: in instantiation of member function 'DoubleMinCostFlow<double>::check_reduced_costs' requested here
   eps=this->check_reduced_costs();
             ^
spams/prox/project.h:4624:13: note: in instantiation of member function 'DoubleMinCostFlow<double>::solve_min_cost' requested here
   _solver->solve_min_cost();
            ^
spams/prox/fista.h:2254:28: note: in instantiation of member function 'DoubleGraphPath<double>::proximal_conv' requested here
                   _graph2.proximal_conv(y.rawX(),lambda,_alt_norm);
                           ^
spams/prox/fista.h:3449:45: note: in instantiation of member function 'FISTA::GraphPathConv<double>::prox' requested here
            case GRAPH_PATH_CONV: reg = new GraphPathConv<T>(param_reg); break;
                                            ^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
                  regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
                                  ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3761:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
   switch (loss) {
           ^
spams/prox/project.h:4019:43: note: in instantiation of member function 'DoubleMinCostFlow<double>::eval_flow_saturate_arc' requested here
         const T saturated_amount = this->eval_flow_saturate_arc(node,arc,target);
                                          ^
spams/prox/project.h:3859:16: note: in instantiation of member function 'DoubleMinCostFlow<double>::saturate_arc' requested here
         this->saturate_arc(i,j);
               ^
spams/prox/project.h:3817:13: note: in instantiation of member function 'DoubleMinCostFlow<double>::refine' requested here
      this->refine(eps);
            ^
spams/prox/project.h:4624:13: note: in instantiation of member function 'DoubleMinCostFlow<double>::solve_min_cost' requested here
   _solver->solve_min_cost();
            ^
spams/prox/fista.h:2254:28: note: in instantiation of member function 'DoubleGraphPath<double>::proximal_conv' requested here
                   _graph2.proximal_conv(y.rawX(),lambda,_alt_norm);
                           ^
spams/prox/fista.h:3449:45: note: in instantiation of member function 'FISTA::GraphPathConv<double>::prox' requested here
            case GRAPH_PATH_CONV: reg = new GraphPathConv<T>(param_reg); break;
                                            ^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
                  regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
                                  ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
In file included from spams/prox/fista.h:24:
spams/prox/project.h:3709:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
   switch (loss) {
           ^
spams/prox/project.h:3696:22: note: in instantiation of member function 'DoubleMinCostFlow<double>::eval_flow_arc' requested here
         cost+=this->eval_flow_arc(i,j);
                     ^
spams/prox/project.h:4545:29: note: in instantiation of member function 'DoubleMinCostFlow<double>::compute_cost' requested here
   const T val=0.5*_solver->compute_cost();
                            ^
spams/prox/fista.h:2265:71: note: in instantiation of member function 'DoubleGraphPath<double>::eval_conv' requested here
                   return const_cast<DoubleGraphPath<T>* >(&_graph2)->eval_conv(x.rawX(),NULL,_alt_norm);
                                                                      ^
spams/prox/fista.h:3449:45: note: in instantiation of member function 'FISTA::GraphPathConv<double>::eval' requested here
            case GRAPH_PATH_CONV: reg = new GraphPathConv<T>(param_reg); break;
                                            ^
spams/prox/fista.h:3719:35: note: in instantiation of function template specialization 'FISTA::setRegularizerVectors<double>' requested here
                  regularizers[i]=setRegularizerVectors(param,graph_st,tree_st,graph_path_st);
                                  ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
         T sec=time.getElapsed();
           ^
spams/prox/fista.h:3620:16: note: in instantiation of function template specialization 'FISTA::ISTA_Generic<double, Vector<double>, Vector<double> >' requested here
               ISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
               ^
spams/prox/fista.h:3735:16: note: in instantiation of function template specialization 'FISTA::solver_aux1<double>' requested here
               solver_aux1(X, alpha0,  alpha, optim_info, regularizers,losses,param);
               ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
         T sec=time.getElapsed();
           ^
spams/prox/fista.h:3624:16: note: in instantiation of function template specialization 'FISTA::FISTA_Generic<double, Vector<double>, Vector<double> >' requested here
               FISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
               ^
spams/prox/fista.h:3735:16: note: in instantiation of function template specialization 'FISTA::solver_aux1<double>' requested here
               solver_aux1(X, alpha0,  alpha, optim_info, regularizers,losses,param);
               ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3477:18: warning: 11 enumeration values not handled in switch: 'GROUPLASSO_L2', 'GROUPLASSO_LINF', 'GROUPLASSO_L2_L1'... [-Wswitch]
         switch (param.regul) {
                 ^
spams/prox/fista.h:3751:35: note: in instantiation of function template specialization 'FISTA::setRegularizerMatrices<double>' requested here
                  regularizers[i]=setRegularizerMatrices(param,alpha0.m(),N,graph_st,tree_st,graph_path_st);
                                  ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
         T sec=time.getElapsed();
           ^
spams/prox/fista.h:3662:16: note: in instantiation of function template specialization 'FISTA::ISTA_Generic<double, Matrix<double>, Vector<double> >' requested here
               ISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
               ^
spams/prox/fista.h:3757:16: note: in instantiation of function template specialization 'FISTA::solver_aux2<double>' requested here
               solver_aux2(X, alpha0,  alpha, optim_info, regularizers,losses,param);
               ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
         T sec=time.getElapsed();
           ^
spams/prox/fista.h:3666:16: note: in instantiation of function template specialization 'FISTA::FISTA_Generic<double, Matrix<double>, Vector<double> >' requested here
               FISTA_Generic(*(losses[numT]),*(regularizers[numT]),alpha0i,alphai,optim_infoi,param);
               ^
spams/prox/fista.h:3757:16: note: in instantiation of function template specialization 'FISTA::solver_aux2<double>' requested here
               solver_aux2(X, alpha0,  alpha, optim_info, regularizers,losses,param);
               ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
         T sec=time.getElapsed();
           ^
spams/prox/fista.h:3796:19: note: in instantiation of function template specialization 'FISTA::ISTA_Generic<double, Matrix<double>, Matrix<double> >' requested here
                  ISTA_Generic(*loss,*regularizer,alpha0,alpha,optim_infoi,param);
                  ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
         T sec=time.getElapsed();
           ^
spams/prox/fista.h:3800:19: note: in instantiation of function template specialization 'FISTA::FISTA_Generic<double, Matrix<double>, Matrix<double> >' requested here
                  FISTA_Generic(*loss,*regularizer,alpha0,alpha,optim_infoi,param);
                  ^
./spams.h:480:10: note: in instantiation of function template specialization 'FISTA::solver<double>' requested here
  FISTA::solver((Matrix<T> &)(*X),(AbstractMatrixB<T> &)(*D),(Matrix<T> &)(*alpha0),(Matrix<T> &)(*alpha),param,(Matrix<T> &)(*duality_gap));
         ^
spams.cpp:3278:34: note: in instantiation of function template specialization '_fistaFlat<double>' requested here
    result = (Matrix< double > *)_fistaFlat< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24,arg25,arg26,arg27,arg28,arg29,arg30,arg31,arg32,arg33,arg34,arg35,arg36,arg37,arg38,arg39);
                                 ^
In file included from spams.cpp:1303:
In file included from ./spams.h:6:
spams/prox/fista.h:3963:21: warning: 6 enumeration values not handled in switch: 'FLOW_LINEAR', 'FLOW_SQUARE_POS', 'FLOW_SQUARE_POS_WEIGHTS'... [-Wswitch]
            switch (loss) {
                    ^
./spams.h:1065:10: note: in instantiation of function template specialization 'FISTA::SepLossPathCoding<double>' requested here
  FISTA::SepLossPathCoding<T>((Matrix<T> &)(*alpha0),(Matrix<T>&)(*alpha),param,loss,&graph,path_out);
         ^
spams.cpp:4813:36: note: in instantiation of function template specialization '_sepCostsPathCoding<double>' requested here
    result = (SpMatrix< double > *)_sepCostsPathCoding< double >(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16,arg17,arg18,arg19);
                                   ^
28 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -mtune=core2 -g -O2  -c structdef.cpp -o structdef.o
In file included from structdef.cpp:6:
In file included from ./structdef.h:11:
./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
  ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
                                                   ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flipflop.so FileSplitter.o R_init_flipflop.o align.o auxiliaryio.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o samples.o spams.o structdef.o -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lcblas -stdlib=libstdc++ -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)

flipflop.Rcheck/flipflop-Ex.timings:

nameusersystemelapsed
flipflop0.7050.0220.728