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CHECK report for flipflop on merida1

This page was generated on 2019-04-16 11:57:15 -0400 (Tue, 16 Apr 2019).

Package 522/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flipflop 1.20.0
Elsa Bernard
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flipflop
Branch: RELEASE_3_8
Last Commit: 5e4e92e
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flipflop
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flipflop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flipflop_1.20.0.tar.gz
StartedAt: 2019-04-15 23:56:14 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:58:05 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 110.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flipflop.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flipflop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flipflop_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flipflop.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.20.0’
* 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 ... WARNING
Found the following significant warnings:
  ./readgroup.h:119:52: warning: field 'orientation' will be initialized after field 'samples' [-Wreorder]
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/flipflop.Rcheck/00install.out’ for details.
* 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 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) ... WARNING
  apparently using $(LAPACK_LIBS) without following $(BLAS_LIBS) in ‘src/Makevars’
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/flipflop.Rcheck/00check.log’
for details.

Installation output

flipflop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flipflop
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flipflop’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -g -O2  -c FileSplitter.cpp -o FileSplitter.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -g -O2  -c align.cpp -o align.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -g -O2  -c bedio.cpp -o bedio.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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:153:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
  int currentreadlen=0;
      ^
samio.cpp:149:7: warning: unused variable 'rangecounter' [-Wunused-variable]
  int rangecounter=1;
      ^
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. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -g -O2  -c samples.cpp -o samples.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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/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:3426:18: warning: 11 enumeration values not handled in switch: 'L1L2', 'L1LINF', 'L1L2_L1'... [-Wswitch]
         switch (param.regul) {
                 ^
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:3761:12: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
   switch (loss) {
           ^
spams/prox/project.h:3709:12: 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: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: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) {
                    ^
28 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -fPIC  -Wall -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 -fopenmp -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lcblas -stdlib=libstdc++ -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/flipflop/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)

Tests output

Example timings

flipflop.Rcheck/flipflop-Ex.timings

nameusersystemelapsed
flipflop0.6750.0120.696