I am getting an error in installing passenger nginx in MAC 10.14.
here are the logs:
src/cxx_supportlib/vendor-modified/boost/atomic/detail/ops_gcc_x86_dcas.hpp:408:16: error:
address argument to atomic builtin cannot be const-qualified
('const volatile
boost::atomics::detail::gcc_dcas_x86_64::storage_type *' (aka
'const volatile unsigned __int128 *') invalid)
return __sync_val_compare_and_swap(&storage, value, value);
^ ~~~~~~~~
1 error generated.
rake aborted!
Command failed with status (1): [c++ -o buildout/support-binaries/AgentFundamentals.o -Isrc/agent -Isrc/cxx_supportlib -Isrc/cxx_supportlib/vendor-copy -Isrc/cxx_supportlib/vendor-modified -Isrc/cxx_supportlib/vendor-modified/libev -Wno-ambiguous-member-template -Isrc/cxx_supportlib/vendor-copy/libuv/include -Isrc/cxx_supportlib/vendor-copy/websocketpp -I/usr/local/opt/openssl/include -D_REENTRANT -I/usr/local/include -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-long-long -Wno-missing-field-initializers -Wno-ambiguous-member-template -fvisibility=hidden -DVISIBILITY_ATTRIBUTE_SUPPORTED -DHAS_ALLOCA_H -DHAS_SFENCE -DHAS_LFENCE -DPASSENGER_DEBUG -DBOOST_DISABLE_ASSERTS -g -fno-limit-debug-info -std=gnu++11 -Wno-unused-local-typedefs -Wno-format-nonliteral -DHAS_UNORDERED_MAP -c src/agent/Shared/Fundamentals/Implementation.cpp]
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/gems/passenger-6.0.2/build/support/cplusplus.rb:53:in `run_compiler'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/gems/passenger-6.0.2/build/support/cplusplus.rb:104:in `compile_cxx'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/gems/passenger-6.0.2/build/support/cplusplus.rb:162:in `block in define_cxx_object_compilation_task'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/bin/ruby_executable_hooks:24:in `eval'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/bin/ruby_executable_hooks:24:in `<main>'
Tasks: TOP => nginx => nginx_without_native_support => buildout/support-binaries/PassengerAgent => buildout/support-binaries/AgentFundamentals.o
(See full trace by running task with --trace)
I already tried this also :
https://github.com/phusion/passenger/issues/2199
Related
I have been trying to compile the R package PET on Fedora 35 (fully updated). It has been archived on CRAN for the past two years or so, but has installed for me before R 4.1.2. I am wondering whether it can be fixed.
I try:
devtools::install_github('cran/PET')
and I get errors, after a bunch of non-alarming messages:
Downloading GitHub repo cran/PET#HEAD
checking for file ‘/tmp/Rtmp2To7Lw/remotesed66e3dbe79/cran-PET-9793d0d/DESCRI✔ checking for file ‘/tmp/Rtmp2To7Lw/remotesed66e3dbe79/cran-PET-9793d0d/DESCRIPTION’
─ preparing ‘PET’:
✔ 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
─ building ‘PET_0.5.1.tar.gz’
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘PET’ ...
** using staged installation
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c Hough.c -o Hough.o
Hough.c: In function ‘Hough4’:
Hough.c:41:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
41 | double theta_min;
| ^~~~~~~~~
Hough.c:40:38: warning: variable ‘y’ set but not used [-Wunused-but-set-variable]
40 | double *costheta,*sintheta,theta,x,y;
| ^
Hough.c: In function ‘Hough3’:
Hough.c:118:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
118 | double theta_min;
| ^~~~~~~~~
Hough.c: In function ‘Hough2’:
Hough.c:173:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
173 | double theta_min;
| ^~~~~~~~~
Hough.c: In function ‘Hough1’:
Hough.c:227:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
227 | double theta_min;
| ^~~~~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c PET_init.c -o PET_init.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c amatrix.c -o amatrix.o
amatrix.c: In function ‘RegulateMatrix’:
amatrix.c:234:10: warning: variable ‘tempVv’ set but not used [-Wunused-but-set-variable]
234 | float *tempVv;
| ^~~~~~
amatrix.c: In function ‘RegulateL1Matrix’:
amatrix.c:289:10: warning: variable ‘tempVv’ set but not used [-Wunused-but-set-variable]
289 | float *tempVv;
| ^~~~~~
amatrix.c: In function ‘GenerateAMatrixColumn’:
amatrix.c:784:9: warning: variable ‘onedivsq2’ set but not used [-Wunused-but-set-variable]
784 | float onedivsq2,psi,pidivDeltaX,costheta,sintheta,of;
| ^~~~~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c art.c -o art.o
art.c: In function ‘FAST_ART’:
art.c:128:10: warning: variable ‘tempXv’ set but not used [-Wunused-but-set-variable]
128 | float *tempXv,*tempBv;
| ^~~~~~
art.c: In function ‘SLOW_ART’:
art.c:239:10: warning: variable ‘tempXv’ set but not used [-Wunused-but-set-variable]
239 | float *tempXv,*tempBv;
| ^~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c calc.c -o calc.o
calc.c: In function ‘BackFilter’:
calc.c:335:19: warning: variable ‘M’ set but not used [-Wunused-but-set-variable]
335 | int i,m,n,mm,nn,M,N,OldHeight,OldWidth;
| ^
calc.c: In function ‘CentralSliceCZ’:
calc.c:700:49: warning: variable ‘rhomin’ set but not used [-Wunused-but-set-variable]
700 | float DC,deltatheta,theta,thetaadj,*realtheta,rhomin,deltarho;
| ^~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cg.c -o cg.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c em.c -o em.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c eval.c -o eval.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c imgtools.c -o imgtools.o
imgtools.c: In function ‘ReadPET’:
imgtools.c:1005:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1005 | size_t result;
| ^~~~~~
imgtools.c: In function ‘ReadFIFHeader’:
imgtools.c:1148:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1148 | size_t result;
| ^~~~~~
imgtools.c: In function ‘ReadFIF’:
imgtools.c:1222:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1222 | size_t result;
| ^~~~~~
imgtools.c: In function ‘ReadAnalyze’:
imgtools.c:1616:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1616 | size_t result;
| ^~~~~~
imgtools.c:1614:21: warning: variable ‘OffSet’ set but not used [-Wunused-but-set-variable]
1614 | float ScaleFactor,OffSet;
| ^~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c iradon.c -o iradon.o
iradon.c: In function ‘iradon’:
iradon.c:271:5: warning: ‘spectrum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
271 | FreeImage(spectrum);
| ^~~~~~~~~~~~~~~~~~~
iradon.c: In function ‘loadFile’:
iradon.c:568:9: warning: ‘list’ may be used uninitialized in this function [-Wmaybe-uninitialized]
568 | return(list);
| ^
iradon.c:404:16: warning: ‘typeF’ may be used uninitialized in this function [-Wmaybe-uninitialized]
404 | OutImage = ReadImage(fileName, typeF);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
iradon.c: In function ‘writeFile’:
iradon.c:684:19: warning: ‘N’ may be used uninitialized in this function [-Wmaybe-uninitialized]
684 | SaveImage=NewFloatImage(fileName, M, N, _RealArray);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iradon.c:684:19: warning: ‘M’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iradon.c:772:5: warning: ‘typeF’ may be used uninitialized in this function [-Wmaybe-uninitialized]
772 | WriteImage(SaveImage, typeF);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c it.c -o it.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c itreadargs.c -o itreadargs.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c misc.c -o misc.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c oradLI.c -o oradLI.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c oradNN.c -o oradNN.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c oradSINC.c -o oradSINC.o
oradSINC.c: In function ‘radonSINC’:
oradSINC.c:52:10: warning: variable ‘idx’ set but not used [-Wunused-but-set-variable]
52 | double idx,mintrig,psi;
| ^~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sparse.c -o sparse.o
sparse.c: In function ‘ReadSIFHeader’:
sparse.c:607:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
607 | size_t result;
| ^~~~~~
sparse.c: In function ‘ReadSIF’:
sparse.c:657:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
657 | size_t result;
| ^~~~~~
sparse.c: In function ‘MeanFilterVector’:
sparse.c:1537:13: warning: variable ‘area’ set but not used [-Wunused-but-set-variable]
1537 | float sum,area,*tempVv,*tempNv,*tempKernM;
|
gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o PET.so Hough.o PET_init.o amatrix.o art.o calc.o cg.o em.o eval.o imgtools.o iradon.o it.o itreadargs.o misc.o oradLI.o oradNN.o oradSINC.o sparse.o -L/usr/lib64/R/lib -lR
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `DebugNiveau'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `IniFile'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `multtemp'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `LogFileName'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `LogFile'; iradon.o (symbol from plugin):(.text+0x0): first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/make/shlib.mk:10: PET.so] Error 1
ERROR: compilation failed for package ‘PET’
* removing ‘/usr/lib64/R/library/PET’
* restoring previous ‘/usr/lib64/R/library/PET’
Warning message:
In i.p(...) :
installation of package ‘/tmp/Rtmp2To7Lw/fileed67b515c13/PET_0.5.1.tar.gz’ had non-zero exit status
Any suggestions as to how i can get this to compile? I need to use the Radon transform on some images.
Thanks!
I am working on a project under Windows and Ubuntu using CMake and CLang. On Ubuntu, I can build it OK with a shell script and could build it using Qt 5.5.1 (Creator 3.5.1). After upgrading to Qt 5.14.0 (Creator 4.11.1), there are over 1200 link errors where doctest cannot be found.
Captured compiler output:
[8/9 4.4/sec] Linking CXX executable test/test_runner
FAILED: : && /opt/clang+llvm-9.0.0-x86_64-linux-gnu-ubuntu-16.04/bin/clang-9 -g -O0 -Wall -pthread --verbose test/CMakeFiles/test_runner.dir/test_runner.cpp.o test/CMakeFiles/test_runner.dir/test.cpp.o -o test/test_runner PSCOM_LIB.a && :
clang version 9.0.0 (https://github.com/llvm-mirror/llvm c62b24f070c9a4bb1a76409e623042a740cac4cd)
Target: x86_64-unknown-linux-gnu
...
"/usr/bin/ld" -z relro --hash-style=gnu --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o test/test_runner /usr/lib/gcc/x86_64-linux-gnu/7.4.0/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/7.4.0/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/7.4.0/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/7.4.0 -L/usr/lib/gcc/x86_64-linux-gnu/7.4.0/../../../x86_64-linux-gnu -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/7.4.0/../../.. -L/opt/clang+llvm-9.0.0-x86_64-linux-gnu-ubuntu-16.04/bin/../lib -L/lib -L/usr/lib test/CMakeFiles/test_runner.dir/test_runner.cpp.o test/CMakeFiles/test_runner.dir/test.cpp.o PSCOM_LIB.a -lgcc --as-needed -lgcc_s --no-as-needed -lpthread -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-linux-gnu/7.4.0/crtend.o /usr/lib/gcc/x86_64-linux-gnu/7.4.0/../../../x86_64-linux-gnu/crtn.o
test/CMakeFiles/test_runner.dir/test_runner.cpp.o: In function `doctest::detail::rawMemoryToString(void const*, unsigned int)':
/home/me/dev/source/vcpkg_pml/vcpkg/installed/x64-linux/include/doctest/doctest.h:2853: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(std::_Ios_Openmode)'
/home/me/dev/source/vcpkg_pml/vcpkg/installed/x64-linux/include/doctest/doctest.h:2854: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'
/home/me/dev/source/vcpkg_pml/vcpkg/installed/x64-linux/include/doctest/doctest.h:2854: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, std::_Setfill<char>)'
/home/me/dev/source/vcpkg_pml/vcpkg/installed/x64-linux/include/doctest/doctest.h:2854: undefined reference to `std::ostream::operator<<(std::ios_base& (*)(std::ios_base&))'
/home/me/dev/source/vcpkg_pml/vcpkg/installed/x64-linux/include/doctest/doctest.h:2856: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, std::_Setw)'
/home/me/dev/source/vcpkg_pml/vcpkg/installed/x64-linux/include/doctest/doctest.h:2856: undefined reference to `std::ostream::operator<<(unsigned int)'
and hundreds of similar errors in several files.
The shell script produces the following output.
"/usr/bin/ld" ... -lstdc++ -lm -lgcc_s -lgcc -lpthread -lc -lgcc_s -lgcc ...
I have no idea why -lstdc++ is added or not but assume that it identifies the required doctest library. Is there an option that can be added to CMakeList.txt to correct this issue?
The following is what I did and the error message:
downloads quazip-0-7-3 from http://quazip.sourceforge.net/index.html, and unzip it to c:\Qt, run the following commands and it gets the error at the end:
C:\Qt\quazip-0.7.3\quazip>where qmake
C:\Qt\5.10.0\msvc2015\bin\qmake.exe
C:\Qt\quazip-0.7.3\quazip>where qmake
C:\Qt\5.10.0\msvc2015\bin\qmake.exe
C:\Qt\quazip-0.7.3\quazip>qmake PREFIX=c:\Qt\quazip
Info: creating stash file C:\Qt\quazip-0.7.3\quazip\.qmake.stash
C:\Qt\quazip-0.7.3\quazip>where make
C:\Program Files (x86)\GnuWin32\bin\make.exe
C:\Qt\quazip-0.7.3\quazip>make
make -f Makefile.Release
make[1]: Entering directory `C:/Qt/quazip-0.7.3/quazip'
Makefile.Release:120: *** missing separator. Stop.
make[1]: Leaving directory `C:/Qt/quazip-0.7.3/quazip'
make: *** [release] Error 2
The following is the Makefile.Release from line 115 to 155, line 120 is "<<":
.SUFFIXES: .c .cpp .cc .cxx
{release}.cpp{release\}.obj::
$(CXX) -c $(CXXFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
{release}.cc{release\}.obj::
$(CXX) -c $(CXXFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
{release}.cxx{release\}.obj::
$(CXX) -c $(CXXFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
{release}.c{release\}.obj::
$(CC) -c $(CFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
{.}.cpp{release\}.obj::
$(CXX) -c $(CXXFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
{.}.cc{release\}.obj::
$(CXX) -c $(CXXFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
{.}.cxx{release\}.obj::
$(CXX) -c $(CXXFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
{.}.c{release\}.obj::
$(CC) -c $(CFLAGS) $(INCPATH) -Forelease\ #<<
$<
<<
Then I use the 'nmake' instead of 'make', but it fails again with different error:
C:\Qt\quazip-0.7.3\quazip>nmake
Microsoft (R) Program Maintenance Utility Version 14.00.24210.0
Copyright (C) Microsoft Corporation. All rights reserved.
"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin\nmake.exe" -f Makefile.Release
Microsoft (R) Program Maintenance Utility Version 14.00.24210.0
Copyright (C) Microsoft Corporation. All rights reserved.
cl -BxC:\Qt\5.10.0\msvc2015\bin\qmake.exe -nologo -Zc:wchar_t -FS -Zc:rvalueCast -Zc:inline -Zc:strictStrings -Zc:throwingNew -O2 -MD -W3 -w34100 -w34189 -w44996 -w44456 -w44457 -w44458 -wd4577 -wd4467 -E ..\..\5.10.0\msvc2015\mkspecs\features\data\dummy.cpp 2>NUL >release\moc_predefs.h
C:\Qt\5.10.0\msvc2015\bin\moc.exe -DUNICODE -D_UNICODE -DWIN32 -DQUAZIP_BUILD -DNOMINMAX -DQT_NO_DEBUG -DQT_CORE_LIB -DNDEBUG -D_WINDLL --compiler-flavor=msvc --include release/moc_predefs.h -IC:/Qt/5.10.0/msvc2015/mkspecs/win32-msvc -IC:/Qt/quazip-0.7.3/quazip -IC:/Qt/quazip-0.7.3/quazip -IC:/Qt/5.10.0/msvc2015/include -IC:/Qt/5.10.0/msvc2015/include/QtCore quagzipfile.h -o release\moc_quagzipfile.cpp
C:\Qt\5.10.0\msvc2015\bin\moc.exe -DUNICODE -D_UNICODE -DWIN32 -DQUAZIP_BUILD -DNOMINMAX -DQT_NO_DEBUG -DQT_CORE_LIB -DNDEBUG -D_WINDLL --compiler-flavor=msvc --include release/moc_predefs.h -IC:/Qt/5.10.0/msvc2015/mkspecs/win32-msvc -IC:/Qt/quazip-0.7.3/quazip -IC:/Qt/quazip-0.7.3/quazip -IC:/Qt/5.10.0/msvc2015/include -IC:/Qt/5.10.0/msvc2015/include/QtCore quaziodevice.h -o release\moc_quaziodevice.cpp
C:\Qt\5.10.0\msvc2015\bin\moc.exe -DUNICODE -D_UNICODE -DWIN32 -DQUAZIP_BUILD -DNOMINMAX -DQT_NO_DEBUG -DQT_CORE_LIB -DNDEBUG -D_WINDLL --compiler-flavor=msvc --include release/moc_predefs.h -IC:/Qt/5.10.0/msvc2015/mkspecs/win32-msvc -IC:/Qt/quazip-0.7.3/quazip -IC:/Qt/quazip-0.7.3/quazip -IC:/Qt/5.10.0/msvc2015/include -IC:/Qt/5.10.0/msvc2015/include/QtCore quazipfile.h -o release\moc_quazipfile.cpp
cl -c -nologo -Zc:wchar_t -FS -Zc:rvalueCast -Zc:inline -Zc:strictStrings -Zc:throwingNew -O2 -MD -W3 -w34100 -w34189 -w44996 -w44456 -w44457 -w44458 -wd4577 -wd4467 -EHsc -DUNICODE -D_UNICODE -DWIN32 -DQUAZIP_BUILD -DNOMINMAX -DQT_NO_DEBUG -DQT_CORE_LIB -DNDEBUG -D_WINDLL -I. -I. -I..\..\5.10.0\msvc2015\include -I..\..\5.10.0\msvc2015\include\QtCore -Irelease -I..\..\5.10.0\msvc2015\mkspecs\win32-msvc -Forelease\ #C:\Users\yhuang\AppData\Local\Temp\nm402C.tmpqioapi.cpp
.\qioapi.cpp(11): fatal error C1083: Cannot open include file: 'stdio.h': No such file or directory
JlCompress.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quaadler32.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quacrc32.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quagzipfile.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quaziodevice.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quazip.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quazipdir.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quazipfile.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quazipfileinfo.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
quazipnewinfo.cpp
..\..\5.10.0\msvc2015\include\QtCore/qglobal.h(45): fatal error C1083: Cannot open include file: 'type_traits': No such file or directory
Generating Code...
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual Studio 14.0
\VC\bin\cl.EXE"' : return code '0x2'
Stop.
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual Studio 14.0
\VC\bin\nmake.exe"' : return code '0x2'
Stop.
Change to the following steps after #hole-otter-rosy's comment, and still got error at the end -
C:\Qt\quazip-0.7.3\quazip>where qmake
C:\Qt\5.10.0\msvc2015\bin\qmake.exe
C:\Qt\quazip-0.7.3\quazip>"C:\Program Files (x86)\Microsoft Visual Studio 14.0\Common7\Tools\vsvars32.bat"
C:\Qt\quazip-0.7.3\quazip>qmake PREFIX=c:\Qt\quazip INCPATH+=C:\Qt\zlib-1.2.11
NOTE: the 'zlib-1.2.11' contains the zlib.h which is required by quazip project.
run 'nmake' and I got the following link error:
C:\Qt\quazip-0.7.3\quazip>nmake
Microsoft (R) Program Maintenance Utility Version 14.00.24210.0
Copyright (C) Microsoft Corporation. All rights reserved.
"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\nmake.exe" -f Makefile.Release
Microsoft (R) Program Maintenance Utility Version 14.00.24210.0
Copyright (C) Microsoft Corporation. All rights reserved.
cl -c -nologo -Zc:wchar_t -FS -Zc:rvalueCast -Zc:inline -Zc:strictStrings -Zc:throwingNew -O2 -MD -W3 -w34100 -w34189 -w44996 -w44456 -w44457 -w44458 -wd4577 -wd4467 -EHsc -DUNICODE -D_UNICODE -DWIN32 -DQUAZIP_BUILD -DNOMINMAX -DQT_NO_DEBUG -DQT_CORE_LIB -DNDEBUG -D_WINDLL -I. -I..\..\zlib-1.2.11 -I. -I..\..\5.10.0\msvc2015\include -I..\..\5.10.0\msvc2015\include\QtCore -Irelease -I..\..\5.10.0\msvc2015\mkspecs\win32-msvc -Forelease\ #C:\Users\yhuang\AppData\Local\Temp\nm2D8C.tmp
qioapi.cpp
JlCompress.cpp
quaadler32.cpp
quacrc32.cpp
quagzipfile.cpp
quaziodevice.cpp
quazip.cpp
quazipdir.cpp
quazipfile.cpp
Generating Code...
cl -c -nologo -Zc:wchar_t -FS -Zc:strictStrings -O2 -MD -W3 -w44456 -w44457 -w44458 -DUNICODE -D_UNICODE -DWIN32 -DQUAZIP_BUILD -DNOMINMAX -DQT_NO_DEBUG -DQT_CORE_LIB -DNDEBUG -D_WINDLL -I. -I..\..\zlib-1.2.11 -I. -I..\..\5.10.0\msvc2015\include -I..\..\5.10.0\msvc2015\include\QtCore -Irelease -I..\..\5.10.0\msvc2015\mkspecs\win32-msvc -Forelease\ #C:\Users\yhuang\AppData\Local\Temp\nm44F3.tmp
unzip.c
zip.c
Generating Code...
cl -c -nologo -Zc:wchar_t -FS -Zc:rvalueCast -Zc:inline -Zc:strictStrings -Zc:throwingNew -O2 -MD -W3 -w34100 -w34189 -w44996 -w44456 -w44457 -w44458 -wd4577 -wd4467 -EHsc -DUNICODE -D_UNICODE -DWIN32 -DQUAZIP_BUILD -DNOMINMAX -DQT_NO_DEBUG -DQT_CORE_LIB -DNDEBUG -D_WINDLL -I. -I..\..\zlib-1.2.11 -I. -I..\..\5.10.0\msvc2015\include -I..\..\5.10.0\msvc2015\include\QtCore -Irelease -I..\..\5.10.0\msvc2015\mkspecs\win32-msvc -Forelease\ #C:\Users\yhuang\AppData\Local\Temp\nm46E8.tmp
moc_quagzipfile.cpp
moc_quaziodevice.cpp
moc_quazipfile.cpp
Generating Code...
link /NOLOGO /DYNAMICBASE /NXCOMPAT /INCREMENTAL:NO /DLL /SUBSYSTEM:WINDOWS /MANIFEST:embed /OUT:release\quazip.dll #C:\Users\yhuang\AppData\Local\Temp\nm4ED5.tmp
Creating library release\quazip.lib and object release\quazip.exp
quaadler32.obj : error LNK2019: unresolved external symbol _adler32 referenced in function "public: __thiscall QuaAdler32::QuaAdler32(void)" (??0QuaAdler32##QAE#XZ)
quacrc32.obj : error LNK2019: unresolved external symbol _crc32 referenced in function "public: __thiscall QuaCrc32::QuaCrc32(void)" (??0QuaCrc32##QAE#XZ)
unzip.obj : error LNK2001: unresolved external symbol _crc32zip.obj : error LNK2001: unresolved external symbol _crc32
quagzipfile.obj : error LNK2019: unresolved external symbol _gzdopen referencedin function "private: bool __thiscall QuaGzipFilePrivate::open<int>(int,class QFlags<enum QIODevice::OpenModeFlag>,class QString &)" (??$open#H#QuaGzipFilePrivate##AAE_NHV?$QFlags#W4OpenModeFlag#QIODevice####AAVQString###Z)
quagzipfile.obj : error LNK2019: unresolved external symbol _gzread referenced in function "protected: virtual __int64 __thiscall QuaGzipFile::readData(char *,__int64)" (?readData#QuaGzipFile##MAE_JPAD_J#Z)
quagzipfile.obj : error LNK2019: unresolved external symbol _gzwrite referencedin function "protected: virtual __int64 __thiscall QuaGzipFile::writeData(char const *,__int64)" (?writeData#QuaGzipFile##MAE_JPBD_J#Z)
quagzipfile.obj : error LNK2019: unresolved external symbol _gzflush referencedin function "public: virtual bool __thiscall QuaGzipFile::flush(void)" (?flush#QuaGzipFile##UAE_NXZ)
quagzipfile.obj : error LNK2019: unresolved external symbol _gzclose referencedin function "public: virtual __thiscall QuaGzipFile::~QuaGzipFile(void)" (??1QuaGzipFile##UAE#XZ)
quagzipfile.obj : error LNK2019: unresolved external symbol _gzopen referenced in function "private: bool __thiscall QuaGzipFilePrivate::open<class QString>(class QString,class QFlags<enum QIODevice::OpenModeFlag>,class QString &)" (??$open#VQString###QuaGzipFilePrivate##AAE_NVQString##V?$QFlags#W4OpenModeFlag#QIODevice####AAV1##Z)
quaziodevice.obj : error LNK2019: unresolved external symbol _deflate referenced in function "public: virtual bool __thiscall QuaZIODevice::flush(void)" (?flush#QuaZIODevice##UAE_NXZ)
zip.obj : error LNK2001: unresolved external symbol _deflatequaziodevice.obj : error LNK2019: unresolved external symbol _deflateEnd referenced in function "public: virtual void __thiscall QuaZIODevice::close(void)" (?close#QuaZIODevice##UAEXXZ)
zip.obj : error LNK2001: unresolved external symbol _deflateEnd
quaziodevice.obj : error LNK2019: unresolved external symbol _inflate referenced in function "protected: virtual __int64 __thiscall QuaZIODevice::readData(char*,__int64)" (?readData#QuaZIODevice##MAE_JPAD_J#Z)
unzip.obj : error LNK2001: unresolved external symbol _inflatequaziodevice.obj : error LNK2019: unresolved external symbol _inflateEnd referenced in function "public: virtual void __thiscall QuaZIODevice::close(void)" (?close#QuaZIODevice##UAEXXZ)
unzip.obj : error LNK2001: unresolved external symbol _inflateEnd
quaziodevice.obj : error LNK2019: unresolved external symbol _deflateInit_ referenced in function "public: virtual bool __thiscall QuaZIODevice::open(class QFlags<enum QIODevice::OpenModeFlag>)" (?open#QuaZIODevice##UAE_NV?$QFlags#W4OpenModeFlag#QIODevice#####Z)
quaziodevice.obj : error LNK2019: unresolved external symbol _inflateInit_ referenced in function "public: virtual bool __thiscall QuaZIODevice::open(class QFlags<enum QIODevice::OpenModeFlag>)" (?open#QuaZIODevice##UAE_NV?$QFlags#W4OpenModeFlag#QIODevice#####Z)
unzip.obj : error LNK2019: unresolved external symbol _inflateInit2_ referencedin function _unzOpenCurrentFile3
unzip.obj : error LNK2019: unresolved external symbol _get_crc_table referencedin function _unzOpenCurrentFile3
zip.obj : error LNK2001: unresolved external symbol _get_crc_table
zip.obj : error LNK2019: unresolved external symbol _deflateInit2_ referenced in function _zipOpenNewFileInZip4_64release\quazip.dll : fatal error LNK1120: 17 unresolved externals
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual Studio 14.0
\VC\BIN\link.EXE"' : return code '0x460'
Stop.
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual Studio 14.0
\VC\BIN\nmake.exe"' : return code '0x2'
Stop.
You are using an MSVC build of Qt and thus cannot use MinGW's make.
The error you get when using nmake indicates that you haven't set up a MSVC build environent. See Build C/C++ code on the command line in the MSVC docs for more information.
I've uploaded my R code on the company's server in order to run it. It was running smoothly on my local R studio and now when I try to run it with Rscript my_script.r I get an enormous amount of errors when trying to install very basic libraries.
if (!require("ggrepel")) {
install.packages("ggrepel", repos="http://cran.fhcrc.org")
library(ggrepel)
}
if (!require("ggplot2")) {
install.packages("ggplot2", repos="http://cran.fhcrc.org")
library("ggplot2")
}
if (!require("gridExtra")) {
install.packages("gridExtra", repos="http://cran.fhcrc.org")
library("gridExtra")
}
This is my code to install the libraries and here's the error:
Loading required package: ggrepel
Installing package into ‘/home/yoda/Rlibs’
(as ‘lib’ is unspecified)
also installing the dependencies ‘tibble’, ‘ggplot2’
trying URL 'http://cran.fhcrc.org/src/contrib/tibble_1.2.tar.gz'
Content type 'application/x-gzip' length 54517 bytes (53 KB)
==================================================
downloaded 53 KB
trying URL 'http://cran.fhcrc.org/src/contrib/ggplot2_2.2.1.tar.gz'
Content type 'application/x-gzip' length 2213308 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'http://cran.fhcrc.org/src/contrib/ggrepel_0.6.5.tar.gz'
Content type 'application/x-gzip' length 568599 bytes (555 KB)
==================================================
downloaded 555 KB
* installing *source* package ‘tibble’ ...
** package ‘tibble’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c matrixToDataFrame.cpp -o matrixToDataFrame.o
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 10; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:91:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<10>’
typename Matrix<RTYPE>::ConstColumn column( m.column(j) ) ;
^
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<10>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<10>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 13; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:92:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<13>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<13>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<13>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 14; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:93:49: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<14>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<14>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<14>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 15; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:94:49: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<15>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<15>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<15>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 16; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:95:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<16>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<16>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<16>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 19; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:96:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<19>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<19>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<19>’
make: *** [matrixToDataFrame.o] Error 1
ERROR: compilation failed for package ‘tibble’
* removing ‘/home/yoda/Rlibs/tibble’
ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
* removing ‘/home/yoda/Rlibs/ggplot2’
* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c repel_boxes.cpp -o repel_boxes.o
g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o ggrepel.so RcppExports.o repel_boxes.o -L/usr/lib64/R/lib -lR
installing to /home/yoda/Rlibs/ggrepel/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘ggplot2’ 1.0.1 was found, but >= 2.0.0 is required by ‘ggrepel’
ERROR: lazy loading failed for package ‘ggrepel’
* removing ‘/home/yoda/Rlibs/ggrepel’
The downloaded source packages are in
‘/tmp/RtmpukzDll/downloaded_packages’
Error in library(ggrepel) : there is no package called ‘ggrepel’
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘ggrepel’
2: In install.packages("ggrepel", repos = "http://cran.fhcrc.org") :
installation of package ‘tibble’ had non-zero exit status
3: In install.packages("ggrepel", repos = "http://cran.fhcrc.org") :
installation of package ‘ggplot2’ had non-zero exit status
4: In install.packages("ggrepel", repos = "http://cran.fhcrc.org") :
installation of package ‘ggrepel’ had non-zero exit status
Execution halted
I have no idea what's going on, and I have to submit this. Is there any way without having sudo rights to download and install an R package?
I am installing dplyr package and I got the following error. Can anybody tell me what should I do to install this package properly?
My session info is:
sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
> devtools::install_github("hadley/dplyr")
Downloading github repo hadley/dplyr#master
Installing dplyr
'/usr/lib64/R/bin/R' --vanilla CMD INSTALL \
'/tmp/RtmpoV0tCa/devtools34c45fda22d7/hadley-dplyr-cd91f33' \
--library='/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1' \
--install-tests
* installing *source* package ‘dplyr’ ...
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/tuple.hpp:33:0,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/allocate.hpp:27,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/buckets.hpp:15,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/table.hpp:10,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/equivalent.hpp:14,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/unordered_map.hpp:17,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered_map.hpp:16,
from ../inst/include/dplyr.h:32,
from RcppExports.cpp:4:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp: In function ‘typename boost::tuples::access_traits<typename boost::tuples::element<N, boost::tuples::cons<HT, TT> >::type>::const_type boost::tuples::get(const boost::tuples::cons<HT, TT>&)’:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp:228:45: warning: typedef ‘cons_element’ locally defined but not used [-Wunused-local-typedefs]
typedef BOOST_DEDUCED_TYPENAME impl::type cons_element;
^
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c address.cpp -o address.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c arrange.cpp -o arrange.o
In file included from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/tuple.hpp:33:0,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/allocate.hpp:27,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/buckets.hpp:15,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/table.hpp:10,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/equivalent.hpp:14,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/unordered_map.hpp:17,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered_map.hpp:16,
from ../inst/include/dplyr.h:32,
from arrange.cpp:1:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp: In function ‘typename boost::tuples::access_traits<typename boost::tuples::element<N, boost::tuples::cons<HT, TT> >::type>::const_type boost::tuples::get(const boost::tuples::cons<HT, TT>&)’:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp:228:45: warning: typedef ‘cons_element’ locally defined but not used [-Wunused-local-typedefs]
typedef BOOST_DEDUCED_TYPENAME impl::type cons_element;
^
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c between.cpp -o between.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c bind.cpp -o bind.o
In file included from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/tuple.hpp:33:0,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/allocate.hpp:27,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/buckets.hpp:15,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/table.hpp:10,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/equivalent.hpp:14,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/unordered_map.hpp:17,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered_map.hpp:16,
from ../inst/include/dplyr.h:32,
from bind.cpp:1:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp: In function ‘typename boost::tuples::access_traits<typename boost::tuples::element<N, boost::tuples::cons<HT, TT> >::type>::const_type boost::tuples::get(const boost::tuples::cons<HT, TT>&)’:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp:228:45: warning: typedef ‘cons_element’ locally defined but not used [-Wunused-local-typedefs]
typedef BOOST_DEDUCED_TYPENAME impl::type cons_element;
^
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o
combine_variables.cpp: In function ‘SEXPREC* combine_vars(std::vector<std::basic_string<char> >, Rcpp::ListOf<Rcpp::Vector<13, Rcpp::PreserveStorage> >)’:
combine_variables.cpp:99:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < vars.size(); ++j) {
^
combine_variables.cpp:135:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (pos < 1 || pos > vars.size())
^
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c distinct.cpp -o distinct.o
In file included from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/tuple.hpp:33:0,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/allocate.hpp:27,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/buckets.hpp:15,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/table.hpp:10,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/equivalent.hpp:14,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/unordered_map.hpp:17,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered_map.hpp:16,
from ../inst/include/dplyr.h:32,
from distinct.cpp:1:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp: In function ‘typename boost::tuples::access_traits<typename boost::tuples::element<N, boost::tuples::cons<HT, TT> >::type>::const_type boost::tuples::get(const boost::tuples::cons<HT, TT>&)’:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp:228:45: warning: typedef ‘cons_element’ locally defined but not used [-Wunused-local-typedefs]
typedef BOOST_DEDUCED_TYPENAME impl::type cons_element;
^
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I"/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c dplyr.cpp -o dplyr.o
In file included from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/tuple.hpp:33:0,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/allocate.hpp:27,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/buckets.hpp:15,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/table.hpp:10,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/detail/equivalent.hpp:14,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered/unordered_map.hpp:17,
from /opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/unordered_map.hpp:16,
from ../inst/include/dplyr.h:32,
from dplyr.cpp:1:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp: In function ‘typename boost::tuples::access_traits<typename boost::tuples::element<N, boost::tuples::cons<HT, TT> >::type>::const_type boost::tuples::get(const boost::tuples::cons<HT, TT>&)’:
/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/BH/include/boost/tuple/detail/tuple_basic.hpp:228:45: warning: typedef ‘cons_element’ locally defined but not used [-Wunused-local-typedefs]
typedef BOOST_DEDUCED_TYPENAME impl::type cons_element;
^
{standard input}: Assembler messages:
{standard input}:695832: Warning: partial line at end of file ignored
{standard input}:695797: Error: invalid operands (*UND* and .gcc_except_table sections) for `-'
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make: *** [dplyr.o] Error 4
ERROR: compilation failed for package ‘dplyr’
* removing ‘/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/dplyr’
Error: Command failed (1)