- Using in the Terminal:
R CMD INSTALL rmetasim-master
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘rmetasim’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'default/America/Montreal'
** libs
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c AlleleObj.cc -o AlleleObj.o
AlleleObj.cc: In member function ‘void SeqAllele::RandomSeq(double, double, double, double)’:
AlleleObj.cc:98:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i<sl)
~^~~
AlleleObj.cc: In member function ‘void SeqAllele::mutate()’:
AlleleObj.cc:174:30: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
b = RandLibObj.unirange(sl - 1);
~~~^~~
AlleleObj.cc: In member function ‘bool SeqAllele::Compare(SeqAllele)’:
AlleleObj.cc:200:19: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (GetSite(i) != obj.GetSite(i))
^
AlleleObj.cc:200:37: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (GetSite(i) != obj.GetSite(i))
^
AlleleObj.cc: In member function ‘virtual void SeqAllele::WriteState(std::ostream&)’:
AlleleObj.cc:215:22: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
sob = GetSite(i);
^
AlleleObj.cc: In member function ‘virtual void SeqAllele::Write(std::ostream&)’:
AlleleObj.cc:227:22: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
sob = GetSite(i);
^
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c AlleleTbl.cc -o AlleleTbl.o
AlleleTbl.cc: In member function ‘void AlleleLookTbl::clear()’:
AlleleTbl.cc:35:13: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
asz = size();
~~~~^~
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BaseObj.cc -o BaseObj.o
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Democlass.cc -o Democlass.o
Democlass.cc: In member function ‘void DemoClass::CompressClass(double)’:
Democlass.cc:127:26: warning: conversion to ‘double’ from ‘std::map<int, PackedIndividual, std::less<int> >::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
if (I.size()>0&&(I.size()<maxind*frac))
~~~~~~^~
Democlass.cc:142:7: warning: conversion to ‘std::map<int, PackedIndividual, std::less<int> >::key_type {aka int}’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
I[i]=tvec[i];
^
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c FastAllele.cc -o FastAllele.o
FastAllele.cc: In member function ‘virtual int InfAlleleTbl::getRandAlleleIndex()’:
FastAllele.cc:80:14: warning: conversion to ‘int’ from ‘std::map<int, Allele, std::less<int> >::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz = A.size();
~~~~~~^~
FastAllele.cc: In member function ‘virtual void InfAlleleTbl::CalcProps()’:
FastAllele.cc:144:12: warning: conversion to ‘int’ from ‘std::map<int, Allele, std::less<int> >::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz=A.size();
~~~~~~^~
FastAllele.cc: In member function ‘virtual void InfAlleleTbl::Write(std::ostream&)’:
FastAllele.cc:419:12: warning: conversion to ‘int’ from ‘std::map<int, Allele, std::less<int> >::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz=A.size();
~~~~~~^~
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c FastSeqAllele.cc -o FastSeqAllele.o
FastSeqAllele.cc: In member function ‘virtual int SeqAlleleTbl::getRandAlleleIndex()’:
FastSeqAllele.cc:44:14: warning: conversion to ‘int’ from ‘std::map<int, SeqAllele, std::less<int> >::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz = A.size();
~~~~~~^~
FastSeqAllele.cc: In member function ‘virtual void SeqAlleleTbl::CalcProps()’:
FastSeqAllele.cc:107:12: warning: conversion to ‘int’ from ‘std::map<int, SeqAllele, std::less<int> >::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz=A.size();
~~~~~~^~
FastSeqAllele.cc: In member function ‘int SeqAlleleTbl::addAlleleState(SequenceType, int)’:
FastSeqAllele.cc:239:23: warning: conversion to ‘int’ from ‘std::vector<char>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
SeqAllele a(seq.size());
~~~~~~~~^~
FastSeqAllele.cc: In member function ‘virtual void SeqAlleleTbl::Write(std::ostream&)’:
FastSeqAllele.cc:350:12: warning: conversion to ‘int’ from ‘std::map<int, SeqAllele, std::less<int> >::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz=A.size();
~~~~~~^~
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Genotype.cc -o Genotype.o
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Landscape.cc -o Landscape.o
Landscape.cc: In member function ‘void Landscape::popsizeset(std::vector<int>&)’:
Landscape.cc:607:14: warning: conversion to ‘int’ from ‘std::vector<int>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
psz=ps.size();
~~~~~~~^~
Landscape.cc: In member function ‘int Landscape::PopSize(int)’:
Landscape.cc:667:18: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
tot = tot + I[i].size();
~~~~^~~~~~~~~~~~~
Landscape.cc:675:14: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
tot = tot + I[i].size();
~~~~^~~~~~~~~~~~~
Landscape.cc: In member function ‘void Landscape::Survive()’:
Landscape.cc:718:29: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
rs = S[e].RandomState();
~~~~~~~~~~~~~~~~^~
Landscape.cc: In member function ‘void Landscape::Reproduce()’:
Landscape.cc:924:40: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (CalculateMaleGameteClassVector(k))
^
Landscape.cc:942:26: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
R[e].SetToState(j);
^
Landscape.cc:945:37: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
noff = R[e].PoissonOffspring(1);
~~~~~~~~~~~~~~~~~~~~~^~~
Landscape.cc:991:22: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
tmpI.SetClass(j);
^
Landscape.cc: In member function ‘void Landscape::Extirpate()’:
Landscape.cc:1070:20: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (p[Habitat(cl)])
^
Landscape.cc: In member function ‘void Landscape::CompressInd()’:
Landscape.cc:1081:12: warning: conversion to ‘int’ from ‘std::vector<DemoClass>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz=I.size();
~~~~~~^~
Landscape.cc: In member function ‘void Landscape::CarryState(size_t, int)’:
Landscape.cc:1096:53: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (densdepdemo == 1) max = int(floor(0.5 + maxsz*1.1));
^~~
Landscape.cc:1102:28: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
numdel = (I[i].size()-max);
~~~~~~~~~~~~^~~~~
Landscape.cc: In member function ‘void Landscape::HabCarry(int)’:
Landscape.cc:1135:20: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
h = Habitat(j);
^
Landscape.cc:1136:44: warning: conversion to ‘__gnu_cxx::__alloc_traits<std::allocator<double> >::value_type {aka double}’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
CarryState(size_t((prop[h])*I[j].size()),j);
~~~~~~~~~^~
Landscape.cc:1136:49: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
CarryState(size_t((prop[h])*I[j].size()),j);
^
Landscape.cc: In member function ‘void Landscape::LambdaAdjust(int)’:
Landscape.cc:1167:31: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
CarryState((int)(I[l].size()*adjrate+0.5),l);
~~~~~~~~~^~
Landscape.cc:1180:34: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
CarryState((int)(I[l].size()*adjrate+0.5),l);
~~~~~~~~~^~
Landscape.cc: In member function ‘void Landscape::LandCarry()’:
Landscape.cc:1195:37: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
CarryState(size_t(pr*I[j].size()),j);
~~~~~~~~~^~
Landscape.cc:1195:42: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
CarryState(size_t(pr*I[j].size()),j);
^
Landscape.cc: In function ‘std::istream& operator>>(std::istream&, Landscape&)’:
Landscape.cc:1354:23: warning: conversion to ‘char’ from ‘std::basic_istream<char>::int_type {aka int}’ may alter its value [-Wconversion]
tc = stream.peek();
~~~~~~~~~~~^~
Landscape.cc: In member function ‘double Landscape_statistics::GenLength()’:
Landscape.cc:1657:49: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
gensiz = gensiz + I[i].GenLength(t)*I[i].size();
~~~~~~~~~^~
Landscape.cc:1658:38: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
totparents= totparents + I[i].size();
~~~~~~~~~^~
Landscape.cc: In member function ‘std::vector<int> Landscape_statistics::Rmat(int)’:
Landscape.cc:1732:24: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
for (p=0;p<Atbls[sz]->getPloidy();p++)
^
Landscape.cc:1737:28: warning: conversion to ‘std::vector<int>::value_type {aka int}’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
retval.push_back(sz);//locus
^
Landscape.cc: In member function ‘void Landscape::LambdaAdjust(int)’:
Landscape.cc:1180:28: warning: ‘l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
CarryState((int)(I[l].size()*adjrate+0.5),l);
^
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c PackedIndividual.cc -o PackedIndividual.o
PackedIndividual.cc: In member function ‘void PackedIndividual::Death(int, AlleleLookTbl&)’:
PackedIndividual.cc:304:18: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (Atbls[i]->getPloidy()==1)
^
PackedIndividual.cc:306:11: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
Atbls[i]->KillAlleleCopy(G[ ((i * MAXPLOIDY) + 0) ],t);
^
PackedIndividual.cc:308:18: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (Atbls[i]->getPloidy()==2)
^
PackedIndividual.cc:310:11: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
Atbls[i]->KillAlleleCopy(G[ ((i * MAXPLOIDY) + 0) ],t);
^
PackedIndividual.cc:311:11: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
Atbls[i]->KillAlleleCopy(G[ ((i * MAXPLOIDY) + 1) ],t);
^
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c RandLib.cc -o RandLib.o
RandLib.cc: In member function ‘int RandLib::unirange(int)’:
RandLib.cc:128:7: warning: unused variable ‘rv’ [-Wunused-variable]
int rv;
^~
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c SiteObj.cc -o SiteObj.o
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c TransMat.cc -o TransMat.o
TransMat.cc: In member function ‘void TransMat::SetRandomToStateVec(double)’:
TransMat.cc:106:19: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
SetToState(i);
^
TransMat.cc:110:36: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
RandLibObj.SetDiscreteLookup(p,sz+1);
~~^~
TransMat.cc: In member function ‘void TransMat::SetRandomFromStateVec()’:
TransMat.cc:128:36: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
RandLibObj.SetDiscreteLookup(p,sz+1);
~~^~
TransMat.cc: In member function ‘size_t TransMat::PoissonOffspring(double)’:
TransMat.cc:149:16: warning: conversion to ‘float’ from ‘double’ may alter its value [-Wfloat-conversion]
val = Value()*eigenratio;
~~~~~~~^~~~~~~~~~~
TransMat.cc: In member function ‘int TransMat::AnyFrom(size_t)’:
TransMat.cc:164:19: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
SetToState(i);
^
TransMat.cc: In function ‘std::ostream& operator<<(std::ostream&, TransMat&)’:
TransMat.cc:299:22: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
TM.SetToState(i);
^
TransMat.cc: In function ‘std::ostream& operator<<(std::ostream&, DemoVec&)’:
TransMat.cc:329:16: warning: conversion to ‘int’ from ‘std::vector<double>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
sz = d.v.size();
~~~~~~~~^~
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rmetasim.cc -o rmetasim.o
rmetasim.cc: In function ‘void R_to_metasim_loci(SEXP, Landscape_statistics&)’:
rmetasim.cc:263:14: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
sl = strlen(ststr);
~~~~~~^~~~~~~
rmetasim.cc:271:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0;j<sl;j++)
~^~~
rmetasim.cc:273:29: warning: conversion to ‘int’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
als.SetSite(ststr[j],j);
^
rmetasim.cc: In function ‘SEXPREC* metasim_to_R_loci(Landscape_statistics&)’:
rmetasim.cc:768:17: warning: conversion to ‘int’ from ‘std::vector<int>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
an = aindx.size();
~~~~~~~~~~^~
rmetasim.cc: In function ‘SEXPREC* l2w(SEXP, SEXP)’:
rmetasim.cc:1186:15: warning: conversion to ‘int’ from ‘std::vector<int>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
l=inmat.size();
~~~~~~~~~~^~
/usr/local/bin/g++ -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 rmetasim.so AlleleObj.o AlleleTbl.o BaseObj.o Democlass.o FastAllele.o FastSeqAllele.o Genotype.o Landscape.o PackedIndividual.o RandLib.o SiteObj.o TransMat.o rmetasim.o -fopenmp -lgomp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmetasim/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘ApplyCarryToStage.Rmd’ using ‘UTF-8’
‘CreatingLandscapes.Rmd’ using ‘UTF-8’
‘Sexuality-and-mating.Rmd’ using ‘UTF-8’
‘Simulating.Rmd’ using ‘UTF-8’
‘rmetasim.Rmd’ using ‘UTF-8’
** testing if installed package can be loaded
* DONE (rmetasim)
Result in a functional install
- Using
devtools::install("rmetasim-master")
Installing rmetasim
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
'/Users/thierry/Dropbox/r_packages/stackr_ressources/testing_functions/test_grur/rmetasim-master' \
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests
* installing *source* package ‘rmetasim’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'default/America/Montreal'
** libs
/usr/local/bin/g++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -std=c++11 -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c AlleleObj.cc -o AlleleObj.o
AlleleObj.cc:15:9: fatal error: RandLib.h: No such file or directory
#include<RandLib.h>
^~~~~~~~~~~
compilation terminated.
make: *** [AlleleObj.o] Error 1
ERROR: compilation failed for package ‘rmetasim’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmetasim’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmetasim’
Error: Command failed (1)
Not installing the package.
I'm sure it's me doing something wrong, but I'm stuck.
Thanks for the help
Thierry