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dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Error while installing functionsdchic #63

Closed Lucas446 closed 1 year ago

Lucas446 commented 1 year ago

Hi,

I am trying to get dcHIC running on macOS 10.15.7.

I choose the conda install, manually installing all dependencies in a conda environment, everything went well.

However, running R CMD INSTALL functionsdchic_1.0.tar.gz yielded: 

`20 warnings and 5 errors generated.
make: *** [/opt/miniconda3/envs/dcHiC_env/lib/R/etc/Makeconf:175: functionsdchic.o] Error 1
ERROR: compilation failed for package ‘functionsdchic’
* removing ‘/opt/miniconda3/envs/dcHiC_env/lib/R/library/functionsdchic’
`

Here are the details:

* installing to library ‘/opt/miniconda3/envs/dcHiC_env/lib/R/library’
* installing *source* package ‘functionsdchic’ ...
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/opt/miniconda3/envs/dcHiC_env/lib/R/include" -DNDEBUG  -I"/opt/miniconda3/envs/dcHiC_env/lib/R/library/Rcpp/include" -I"/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/opt/miniconda3/envs/dcHiC_env/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/miniconda3/envs/dcHiC_env/include -fdebug-prefix-map=/Users/builder/ktietz/conda/conda-bld/r-base_1557826964646/work=/usr/local/src/conda/r-base-3.6.0 -fdebug-prefix-map=/opt/miniconda3/envs/dcHiC_env=/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/Rcpp/include/Rcpp.h:55:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/Rcpp/include/Rcpp/StringTransformer.h:30:40: warning: 'unary_function<const char *, const char *>' is deprecated [-Wdeprecated-declarations]
        class StringTransformer : public std::unary_function<const char*, const char*>{
                                              ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<const char *, const char *>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
                            ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__config:854:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                        ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__config:839:49: note: expanded from macro '_LIBCPP_DEPRECATED'
      define _LIBCPP_DEPRECATED __attribute__((deprecated))
                                                ^
1 warning generated.
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/opt/miniconda3/envs/dcHiC_env/lib/R/include" -DNDEBUG  -I"/opt/miniconda3/envs/dcHiC_env/lib/R/library/Rcpp/include" -I"/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/opt/miniconda3/envs/dcHiC_env/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/miniconda3/envs/dcHiC_env/include -fdebug-prefix-map=/Users/builder/ktietz/conda/conda-bld/r-base_1557826964646/work=/usr/local/src/conda/r-base-3.6.0 -fdebug-prefix-map=/opt/miniconda3/envs/dcHiC_env=/usr/local/src/conda-prefix  -c functionsdchic.cpp -o functionsdchic.o
In file included from functionsdchic.cpp:9:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/Rcpp/include/Rcpp.h:55:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/Rcpp/include/Rcpp/StringTransformer.h:30:40: warning: 'unary_function<const char *, const char *>' is deprecated [-Wdeprecated-declarations]
        class StringTransformer : public std::unary_function<const char*, const char*>{
                                              ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<const char *, const char *>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
                            ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__config:854:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                        ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__config:839:49: note: expanded from macro '_LIBCPP_DEPRECATED'
      define _LIBCPP_DEPRECATED __attribute__((deprecated))
                                                ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:1:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Core:540:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:2:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/LU:47:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Jacobi:29:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Cholesky:43:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/QR:15:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Householder:27:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/QR:48:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:5:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/SVD:48:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:6:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Geometry:58:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Dense:7:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Eigenvalues:58:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/SparseCore:66:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/OrderingMethods:71:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/SparseCholesky:43:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/SparseQR:34:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/CholmodSupport:45:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:10:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/opt/miniconda3/envs/dcHiC_env/lib/R/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    pragma clang diagnostic pop
                             ^
In file included from functionsdchic.cpp:12:
In file included from ./BMAcc.h:6:
In file included from ./FBM.h:10:
In file included from ./mmap.hpp:24:
In file included from ./page.hpp:27:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/unistd.h:655:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/gethostuuid.h:39:17: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int gethostuuid(uuid_t, const struct timespec *) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_NA);
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from functionsdchic.cpp:12:
In file included from ./BMAcc.h:6:
In file included from ./FBM.h:10:
In file included from ./mmap.hpp:24:
In file included from ./page.hpp:27:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/unistd.h:662:27: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      getsgroups_np(int *, uuid_t);
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from functionsdchic.cpp:12:
In file included from ./BMAcc.h:6:
In file included from ./FBM.h:10:
In file included from ./mmap.hpp:24:
In file included from ./page.hpp:27:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/unistd.h:664:27: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      getwgroups_np(int *, uuid_t);
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from functionsdchic.cpp:12:
In file included from ./BMAcc.h:6:
In file included from ./FBM.h:10:
In file included from ./mmap.hpp:24:
In file included from ./page.hpp:27:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/unistd.h:727:31: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      setsgroups_np(int, const uuid_t);
                                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from functionsdchic.cpp:12:
In file included from ./BMAcc.h:6:
In file included from ./FBM.h:10:
In file included from ./mmap.hpp:24:
In file included from ./page.hpp:27:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/unistd.h:729:31: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      setwgroups_np(int, const uuid_t);
                                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
functionsdchic.cpp:155:65: warning: 'bind2nd<std::minus<double>, double>' is deprecated [-Wdeprecated-declarations]
    std::transform(colv.begin(), colv.end(), diff.begin(), std::bind2nd(std::minus<double>(), mean));
                                                                ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__functional/binder2nd.h:44:1: note: 'bind2nd<std::minus<double>, double>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__config:854:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                        ^
/opt/miniconda3/envs/dcHiC_env/bin/../include/c++/v1/__config:839:49: note: expanded from macro '_LIBCPP_DEPRECATED'
      define _LIBCPP_DEPRECATED __attribute__((deprecated))
                                                ^

Thank you very much for your help, Best, Tanguy

ay-lab commented 1 year ago

Hello,

I just tried running the installation on an Intel Mac running MacOS 10.15.7 Catalina and it worked for me. Looking into the issue, it seems like something with an Rcpp release: can you try this?

Lucas446 commented 1 year ago

Hi,

I apply the fix to Rcpp but still same errors. Could you tell me what the output of conda list from your install on MacOS 10.15.7 Catalina ? So I can compare the version of dependencies.

If you think about anything else :)

Thanks a lot, Best,

ay-lab commented 1 year ago

I'm using conda 4.14.0. See my conda list here:

condaenv.txt

Lucas446 commented 1 year ago

Hi,

I decided to manually install the R package directly on Rstudio. I still got BH/boost errors and Rcpp errors while compiling hashmap and functionsdchic.

However it worked by downgrading the version of BH & Rcpp packages to 1.72.0-3 and 1.0.8 respectively.

Thank you for your help.