Unable to install SPP on Linux.
Ajeet Mandal
Last login: Thu Jul 20 23:21:33 on ttys001
Ajeets-MacBook-Pro:~ Ajeet$ R CMD INSTALL spp-1.14.tar.gz
Warning in untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘spp’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for BZ2_bzDecompressInit in -lbz2... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking how to run the C++ preprocessor... g++ -E
checking for a sed that does not truncate output... /usr/bin/sed
checking for Boost headers version >= 1.41.0... yes
checking for Boost's header version... 1_64
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fPIC -Wall -g -O2 -c bed2vector.cpp -o bed2vector.o
In file included from bed2vector.cpp:1:
In file included from ./pc.h:4:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ext/hash_map:213:5: warning:
Use of the header <ext/hash_map> is deprecated. Migrate to <unordered_map>
[-W#warnings]
# warning Use of the header <ext/hash_map> is deprecated. Migrate to ...
^
bed2vector.cpp:118:25: error: reference to 'hash' is ambiguous
hash_map<string, int, hash<string>,equal_to<string> > cind_map;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:3171:29: note:
candidate found by name lookup is 'std::__1::hash'
template <class _Tp> struct hash;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ext/__hash:22:54: note:
candidate found by name lookup is '__gnu_cxx::hash'
template <typename _Tp> struct _LIBCPP_TYPE_VIS_ONLY hash { };
^
bed2vector.cpp:118:30: error: unexpected type name 'string': expected expression
hash_map<string, int, hash<string>,equal_to<string> > cind_map;
^
bed2vector.cpp:163:29: error: reference to 'hash' is ambiguous
hash_map<string, int, hash<string>,equal_to<string> >::const_itera...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:3171:29: note:
candidate found by name lookup is 'std::__1::hash'
template <class _Tp> struct hash;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ext/__hash:22:54: note:
candidate found by name lookup is '__gnu_cxx::hash'
template <typename _Tp> struct _LIBCPP_TYPE_VIS_ONLY hash { };
^
bed2vector.cpp:163:34: error: unexpected type name 'string': expected expression
hash_map<string, int, hash<string>,equal_to<string> >::const_itera...
^
bed2vector.cpp:165:10: error: use of undeclared identifier 'li'
if(li==cind_map.end()) {
^
bed2vector.cpp:165:14: error: use of undeclared identifier 'cind_map'
if(li==cind_map.end()) {
^
bed2vector.cpp:169:2: error: use of undeclared identifier 'cind_map'
cind_map[chr]=cind;
^
bed2vector.cpp:176:7: error: use of undeclared identifier 'li'
cind=li->second;
^
bed2vector.cpp:254:25: error: reference to 'hash' is ambiguous
hash_map<string, int, hash<string>,equal_to<string> > cind_map;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:3171:29: note:
candidate found by name lookup is 'std::__1::hash'
template <class _Tp> struct hash;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ext/__hash:22:54: note:
candidate found by name lookup is '__gnu_cxx::hash'
template <typename _Tp> struct _LIBCPP_TYPE_VIS_ONLY hash { };
^
bed2vector.cpp:254:30: error: unexpected type name 'string': expected expression
hash_map<string, int, hash<string>,equal_to<string> > cind_map;
^
bed2vector.cpp:296:29: error: reference to 'hash' is ambiguous
hash_map<string, int, hash<string>,equal_to<string> >::const_itera...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:3171:29: note:
candidate found by name lookup is 'std::__1::hash'
template <class _Tp> struct hash;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ext/__hash:22:54: note:
candidate found by name lookup is '__gnu_cxx::hash'
template <typename _Tp> struct _LIBCPP_TYPE_VIS_ONLY hash { };
^
bed2vector.cpp:296:34: error: unexpected type name 'string': expected expression
hash_map<string, int, hash<string>,equal_to<string> >::const_itera...
^
bed2vector.cpp:298:10: error: use of undeclared identifier 'li'
if(li==cind_map.end()) {
^
bed2vector.cpp:298:14: error: use of undeclared identifier 'cind_map'
if(li==cind_map.end()) {
^
bed2vector.cpp:302:2: error: use of undeclared identifier 'cind_map'
cind_map[chr]=cind;
^
bed2vector.cpp:311:7: error: use of undeclared identifier 'li'
cind=li->second;
^
bed2vector.cpp:432:25: error: reference to 'hash' is ambiguous
hash_map<string, int, hash<string>,equal_to<string> > cind_map;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:3171:29: note:
candidate found by name lookup is 'std::__1::hash'
template <class _Tp> struct hash;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ext/__hash:22:54: note:
candidate found by name lookup is '__gnu_cxx::hash'
template <typename _Tp> struct _LIBCPP_TYPE_VIS_ONLY hash { };
^
bed2vector.cpp:432:30: error: unexpected type name 'string': expected expression
hash_map<string, int, hash<string>,equal_to<string> > cind_map;
^
bed2vector.cpp:476:29: error: reference to 'hash' is ambiguous
hash_map<string, int, hash<string>,equal_to<string> >::const_itera...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/memory:3171:29: note:
candidate found by name lookup is 'std::__1::hash'
template <class _Tp> struct hash;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ext/__hash:22:54: note:
candidate found by name lookup is '__gnu_cxx::hash'
template <typename _Tp> struct _LIBCPP_TYPE_VIS_ONLY hash { };
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
1 warning and 20 errors generated.
make: *** [bed2vector.o] Error 1
ERROR: compilation failed for package ‘spp’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/spp’
Ajeets-MacBook-Pro:~ Ajeet$
Jin
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