Open Quentin97433333 opened 1 year ago
same problem here:
you can try this
devtools::install_github("jspidlen/flowUtils")
devtools::install_github("JhuangLab/CytoTree")
Having an issue installing as well. I have installed flowUtils but still get the following error:
> devtools::install_github("JhuangLab/CytoTree")
Downloading GitHub repo JhuangLab/CytoTree@HEAD
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/kb/43q118t50tn_nf4ctrlp3t240000gn/T/RtmpiwaKBq/remotes420729b58126/JhuangLab-CytoTree-1c60ff8/DESCRIPTION’ ...
─ preparing ‘CytoTree’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘CytoTree_1.0.3.tar.gz’
* installing *source* package ‘CytoTree’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:26: error: no template named 'numeric_limits'
bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:60: error: no template named 'numeric_limits'
bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:18: error: no template named 'numeric_limits'
int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:50: error: no template named 'numeric_limits'
int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:648:17: error: no template named 'numeric_limits'
static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:25: error: no template named 'numeric_limits'
return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:58: error: no template named 'numeric_limits'
return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:661:16: error: no template named 'numeric_limits'
using _Lim = numeric_limits<_IntT>;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:664:12: error: use of undeclared identifier '_Lim'
return _Lim::max();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:665:21: error: use of undeclared identifier '_Lim'
} else if (__r <= _Lim::lowest()) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:666:12: error: use of undeclared identifier '_Lim'
return _Lim::min();
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:490:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/search.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/concepts:134:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:138:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int abs(int) __pure2;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:853:1: error: declaration conflicts with target of using declaration already in scope
abs(const complex<_Tp>& __c)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: target of using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:9: note: using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:910:16: error: reference to unresolved using declaration
return abs(__c.real());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:912:16: error: reference to unresolved using declaration
return abs(__c.imag());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:969:16: error: reference to unresolved using declaration
__re = abs(__re);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1022:29: error: reference to unresolved using declaration
return complex<_Tp>(log(abs(__x)), arg(__x));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1049:23: error: reference to unresolved using declaration
return polar(sqrt(abs(__x)), arg(__x) / _Tp(2));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1174:33: error: reference to unresolved using declaration
return complex<_Tp>(abs(__x.real()), __x.imag());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘CytoTree’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/CytoTree’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/kb/43q118t50tn_nf4ctrlp3t240000gn/T//RtmpiwaKBq/file42074b31fb2e/CytoTree_1.0.3.tar.gz’ had non-zero exit status
` ``
Hi, Hello, I am having trouble downloading the cytotree package, I receive this message " A version of this package for your version of R may be available elsewhere, see ideas.