matthiasheinig
commented
6 years ago Hi Rinaldo,
could you please try installing with devtools and see what you get there?
install.packages("devtools") devtools::install_github("matthiasheinig/histoneHMM")
Best, Matthias
Matthias Heinig Institute of Computational Biology - http://icb.helmholtz-muenchen.de
Am 12.04.2018 um 00:16 schrieb Rinaldo Catta-Preta notifications@github.com:
I tried to install it today, but it failed with the following message. Could you please address it? Thanks!
install.packages("~/Downloads/histoneHMM_1.6.tar.gz", repos = NULL, type = "source") Installing package into ‘/Users/rinaldo/Rlibs’ (as ‘lib’ is unspecified)
• installing source package ‘histoneHMM’ ... * libs /usr/local/clang4/bin/clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG gsl-config --cflags /Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()" -I/usr/local/include -g -O2 -stdlib=libc++ -fPIC -Wall -g -O2 -c densities.cpp -o densities.o In file included from densities.cpp:1: In file included from ./densities.h:26: In file included from /Users/rinaldo/Rlibs/Rcpp/include/Rcpp.h:27: In file included from /Users/rinaldo/Rlibs/Rcpp/include/RcppCommon.h:138: /Users/rinaldo/Rlibs/Rcpp/include/Rcpp/exceptions.h:106:53: warning: all paths through this function will call itself [-Winfinite-recursion] inline void warning(const std::string& message) { // #nocov start ^ In file included from densities.cpp:1: ./densities.h:80:8: warning: 'Zero::initialize' hides overloaded virtual function [-Woverloaded-virtual] void initialize(); ^ ./densities.h:58:16: note: hidden overloaded virtual function 'Density::initialize' declared here: different number of parameters (2 vs 0) virtual void initialize(double weight, int T) = 0; ^ densities.cpp:61:34: warning: all paths through this function will call itself [-Winfinite-recursion] double LogNormal::density(int t) { ^ densities.cpp:829:33: warning: all paths through this function will call itself [-Winfinite-recursion] double Zinba::logdensity(int t) { ^ densities.cpp:1218:13: warning: unused variable 'jN' [-Wunused-variable] int ti, jN, k, kmax; ^ densities.cpp:2241:12: warning: unused variable 'negbino' [-Wunused-variable] double negbino; ^ densities.cpp:2268:1: warning: control may reach end of non-void function [-Wreturn-type] }; ^ densities.cpp:2341:18: warning: unused variable 'jN' [-Wunused-variable] int k, kmax, jN; ^ densities.cpp:2572:13: warning: unused variable 'jN' [-Wunused-variable] int ti, jN, k, kmax; ^ In file included from densities.cpp:1: In file included from ./densities.h:26: In file included from /Users/rinaldo/Rlibs/Rcpp/include/Rcpp.h:69: /Users/rinaldo/Rlibs/Rcpp/include/Rcpp/Nullable.h:108:30: error: too many arguments to function call, expected 0, have 1 return Rf_isNull(m_sexp);
/Users/rinaldo/Rlibs/Rcpp/include/Rcpp/Nullable.h:117:22: note: in instantiation of member function 'Rcpp::Nullable<Rcpp::Vector<14, PreserveStorage> >::Rf_isNull' requested here return ! isNull(); ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1261:18: note: expanded from macro 'isNull' #define isNull Rf_isNull ^ /Users/rinaldo/Rlibs/Rcpp/include/Rcpp/sugar/functions/sample.h:403:15: note: in instantiation of member function 'Rcpp::Nullable<Rcpp::Vector<14, PreserveStorage> >::isNotNull' requested here if (probs.isNotNull()) { ^ /Users/rinaldo/Rlibs/Rcpp/include/Rcpp/Nullable.h:106:9: note: 'Rf_isNull' declared here inline bool isNull() const { ^ 9 warnings and 1 error generated. make: *** [densities.o] Error 1 ERROR: compilation failed for package ‘histoneHMM’ • removing ‘/Users/rinaldo/Rlibs/histoneHMM’ Warning in install.packages : installation of package ‘/Users/rinaldo/Downloads/histoneHMM_1.6.tar.gz’ had non-zero exit status sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.4.4 tools_3.4.4 yaml_2.1.18 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.
Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671
cattapre
dfv
AshwinKoppayi
I tried to install it today, but it failed with the following message. Could you please address it? Thanks!
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] compiler_3.4.4 tools_3.4.4 yaml_2.1.18