I am new to this and I am trying to install Rhipe-0.74 on centos 6.2. I am getting following error.
[root#hadoop-master Rhipe]# R CMD INSTALL Rhipe_0.74.0.tar.gz
* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘Rhipe’ ...
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I. -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DUSEAUTOSHORT -DHAVE_UINTPTR_T `/usr/lib64/R/bin/R CMD config --cppflags` `pkg-config --cflags protobuf` -c rexp.pb.cc -o rexp.pb.o
In file included from rexp.pb.cc:4:
rexp.pb.h:17:2: error: #error This file was generated by an older version of protoc which is
rexp.pb.h:18:2: error: #error incompatible with your Protocol Buffer headers. Please
rexp.pb.h:19:2: error: #error regenerate this file with a newer version of protoc.
In file included from rexp.pb.cc:4:
rexp.pb.h: In member function ‘void REXP::clear_rawvalue()’:
rexp.pb.h:672: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘void REXP::set_rawvalue(const std::string&)’:
rexp.pb.h:682: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘void REXP::set_rawvalue(const char*)’:
rexp.pb.h:689: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘void REXP::set_rawvalue(const void*, size_t)’:
rexp.pb.h:696: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘std::string* REXP::mutable_rawvalue()’:
rexp.pb.h:703: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘std::string* REXP::release_rawvalue()’:
rexp.pb.h:710: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h:714: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘void STRING::clear_strval()’:
rexp.pb.h:853: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘void STRING::set_strval(const std::string&)’:
rexp.pb.h:863: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘void STRING::set_strval(const char*)’:
rexp.pb.h:870: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘void STRING::set_strval(const char*, size_t)’:
rexp.pb.h:877: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘std::string* STRING::mutable_strval()’:
rexp.pb.h:884: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h: In member function ‘std::string* STRING::release_strval()’:
rexp.pb.h:891: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.h:895: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.cc: In member function ‘void REXP::SharedCtor()’:
rexp.pb.cc:256: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.cc: In member function ‘void REXP::SharedDtor()’:
rexp.pb.cc:265: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.cc: In member function ‘virtual void REXP::Clear()’:
rexp.pb.cc:296: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.cc: In member function ‘void STRING::SharedCtor()’:
rexp.pb.cc:905: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.cc: In member function ‘void STRING::SharedDtor()’:
rexp.pb.cc:915: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
rexp.pb.cc: In member function ‘virtual void STRING::Clear()’:
rexp.pb.cc:945: error: ‘kEmptyString’ is not a member of ‘google::protobuf::internal’
make: *** [rexp.pb.o] Error 1
ERROR: compilation failed for package ‘Rhipe’
* removing ‘/usr/lib64/R/library/Rhipe’
As I understood the problem is due to multiple protobuf installation. I googled it but still couldn't resolve the issue. Please help me to solve this. Any help will be appreciated. Thank you in advance.
Maybe it's a bit late, but I was having the same issue and managed to install it by using protobuf version 2.5.0 and RHipe v0.75.1.3 in CentOS 7.
You can download this version of protobuf from here. Copy the tar.gz within /usr/local/lib and follow the instructions in the README (basically, unzip it and execute./configure, make and make install).
After that, set the required hadoop environment variables (PKG_CONFIG_PATH needs to point to /usr/local/lib/pkgconfig, or to the folder where you installed Protobuf). Finally, install the RHipe package. You can download older versions of RHipe from here.
Cheers.
Related
I'm trying to link against the QPid Proton library, using static libs, and am getting lots of link errors. I am able to build with the shared libraries, but for this project we need to use static libs.
Here's the CMake file:
cmake_minimum_required(VERSION 3.0.0)
project(test-qpid VERSION 0.1.0)
include(CTest)
enable_testing()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -no-pie " )
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -v -std=c++17 -lpthread -static-libgcc -static-libstdc++ -fdiagnostics-color=auto")
set(THREADS_PREFER_PTHREAD_FLAG ON)
add_library(libpthread STATIC IMPORTED)
set_target_properties(libpthread PROPERTIES IMPORTED_LOCATION /usr/lib/x86_64-linux-gnu/libpthread.a)
set_target_properties(libpthread PROPERTIES INTERFACE_INCLUDE_DIRECTORIES /usr/include)
add_executable(test-qpid main.cpp)
find_library(QPID_PROTON_CORE NAMES qpid-proton-core-static)
if (NOT QPID_PROTON_CORE)
message(FATAL_ERROR, "QPid Proton core static library not found")
endif()
find_library(QPID_PROTON_PROACTOR NAMES qpid-proton-proactor-static)
if (NOT QPID_PROTON_PROACTOR)
message(FATAL_ERROR, "QPid Proton proactor static library not found")
endif()
find_library(QPID_PROTON NAMES qpid-proton-static)
if (NOT QPID_PROTON)
message(FATAL_ERROR, "QPid Proton static library not found")
endif()
find_library(QPID_PROTON_CPP NAMES qpid-proton-cpp-static)
if (NOT QPID_PROTON_CPP)
message(FATAL_ERROR, "QPid Proton CPP static library not found")
endif()
set(CPACK_PROJECT_NAME ${PROJECT_NAME})
set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
include_directories("/usr/local/include")
set(LIBS ${QPID_PROTON_CORE} ${QPID_PROTON} ${QPID_PROTON_PROACTOR} ${QPID_PROTON_CPP})
target_link_libraries(test-qpid ${LIBS} libpthread)
include(CPack)
Here is a snippet of the output I'm seeing (there are lots more, which I've omitted for brevity):
-L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lpthread CMakeFiles/test-qpid.dir/main.cpp.o /usr/local/lib/libqpid-proton-core-static.a /usr/local/lib/libqpid-proton-static.a /usr/local/lib/libqpid-proton-proactor-static.a /usr/local/lib/libqpid-proton-cpp-static.a /usr/lib/x86_64-linux-gnu/libpthread.a -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/9/crtend.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::close()':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:65: undefined reference to `pn_connection_close'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::error() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:171: undefined reference to `pn_connection_remote_condition'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::transport() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:52: undefined reference to `pn_connection_transport'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::open(proton::connection_options const&)':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:61: undefined reference to `pn_connection_open'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::virtual_host[abi:cxx11]() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:71: undefined reference to `pn_connection_remote_hostname'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::container_id[abi:cxx11]() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:75: undefined reference to `pn_connection_remote_container'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::user[abi:cxx11]() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:79: undefined reference to `pn_connection_transport'
[build] /usr/bin/ld: /home/user/src/qpid-proton/cpp/src/connection.cpp:79: undefined reference to `pn_transport_get_user'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::sessions() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:93: undefined reference to `pn_session_head'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::receivers() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:97: undefined reference to `pn_link_head'
[build] /usr/bin/ld: /home/user/src/qpid-proton/cpp/src/connection.cpp:101: undefined reference to `pn_link_next'
[build] /usr/bin/ld: /home/user/src/qpid-proton/cpp/src/connection.cpp:99: undefined reference to `pn_link_is_receiver'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::senders() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:107: undefined reference to `pn_link_head'
[build] /usr/bin/ld: /home/user/src/qpid-proton/cpp/src/connection.cpp:111: undefined reference to `pn_link_next'
[build] /usr/bin/ld: /home/user/src/qpid-proton/cpp/src/connection.cpp:109: undefined reference to `pn_link_is_sender'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::open_session(proton::session_options const&)':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:121: undefined reference to `pn_session'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::default_session()':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:133: undefined reference to `pn_session'
[build] /usr/bin/ld: /home/user/src/qpid-proton/cpp/src/connection.cpp:134: undefined reference to `pn_session_open'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::max_frame_size() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:175: undefined reference to `pn_connection_transport'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::max_sessions() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:179: undefined reference to `pn_connection_transport'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::idle_timeout() const':
[build] /home/user/src/qpid-proton/cpp/src/connection.cpp:183: undefined reference to `pn_connection_transport'
[build] /usr/bin/ld: /usr/local/lib/libqpid-proton-cpp-static.a(connection.cpp.o): in function `proton::connection::desired_capabilities() const':
I've been Googling for answers for days and have gotten nowhere. If anyone has any experience with QPid Proton I'd greatly appreciate some suggestions.
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?
I have a very strange problem I create an application that use QNetworkAcessManager to download an HTML page and get the data from this page I release my application to use it on my second laptop on the same wireless connection but it not works.
on my computer, after releasing the app and use windeploy.exe to get all the dll file for this release exe I try to use it on my computer which has QT and developed on it it works fine and get the data in the file.
the problem comes when I use it on another computer the app works but when I press the button to get the data it gets nothing just empty file
so any help for this problem
this the code which I use normal QNetworkAcessManager code to get HTML page data
this code in the button to get the data
manager->clearAccessCache();
manager->clearConnectionCache();
if (reply != nullptr)
delete reply;
reply = manager->get(QNetworkRequest(QUrl("https://normalpage.html")));
connect(reply, SIGNAL(readyRead()), this, SLOT(readyRead()));
connect(reply, SIGNAL(finished()), this, SLOT(Finish()));
readyread
void MainWindow::readyRead()
{
data.append(reply->readAll());
}
finish function I get the data of type QByteArray and use it to get the data from it the function is long
I was having this problem for about two months but I was in hurry so I used libcurl with QProcess to get this HTML page data but I now I want to know what cause this problem
update
I used the code in my main.cpp to get all the Qt warnings and errors in a file as mention in the comment by Macias and I get this into the file I used append to the file so I can get all the error it comes and I got some warnings from QSslSocket if anyone can check these warnings and see if it cause the problem as I don't know
Error file
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
)
))
Warning: QSslSocket: cannot call unresolved function SSLv23_client_method ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_CTX_new ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_library_init ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSLv23_client_method ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_CTX_new ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_library_init ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
but in the working computer I got this warrnings
Warning: QSslSocket: cannot resolve SSL_set_alpn_protos ((null):0, (null))
Warning: QSslSocket: cannot resolve SSL_CTX_set_alpn_select_cb ((null):0, (null))
Warning: QSslSocket: cannot resolve SSL_get0_alpn_selected ((null):0, (null))
Warning: QSslSocket: cannot resolve SSL_set_alpn_protos ((null):0, (null))
Warning: QSslSocket: cannot resolve SSL_CTX_set_alpn_select_cb ((null):0, (null))
Warning: QSslSocket: cannot resolve SSL_get0_alpn_selected ((null):0, (null))
Update
when i add the new dll files in the folder excutable file it give me this warrnings
Warning: QSslSocket: cannot call unresolved function SSLv23_client_method ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_CTX_new ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_library_init ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
connect the reply to the error signal
connect(reply, SIGNAL(error(QNetworkReply::NetworkError)), this, SLOT(Error(QNetworkReply::NetworkError)));
and the slot is here
void MainWindow::Error(QNetworkReply::NetworkError Myerror)
{
qDebug() << "QNetworkReply::NetworkError = " << Myerror;
}
this what i get after connect error signal and the attribute
Warning: QSslSocket: cannot call unresolved function SSLv23_client_method ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_CTX_new ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function SSL_library_init ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
Warning: QSslSocket: cannot call unresolved function ERR_get_error ((null):0, (null))
Debug: QNetworkReply::NetworkError = QNetworkReply::NetworkError(UnknownNetworkError) ((null):0, (null))
Debug: Attribute in finish slot = QVariant(Invalid) ((null):0, (null))
when I added the three dlls file to the release folder on my computer which the app i working without them i got this error
when i go to the path of C:\AppServ\Apache24\bin and copied this dlls (libeay32.dll and ssleay32.dll) from this folder instead of the others i downloaded from the dll website it finally it works but what is the difference between both in the appchace folder and that are download from website?
thanks in advance
Make sure that you have libeay32.dll, libssl32.dll and ssleay32.dll libs in your deployment folder. If not just copy them next to your *.exe
windeployqt tool does not include these libs.
EDIT:
Your error is propably caused by incopatible version of openSSL library.
Version in use at compile time is different from this used at run-time. You can easily check it out. Add these lines after QApplication creation in main.cpp:
qDebug() << "SslSupport: " << QSslSocket::supportsSsl();
qDebug() << "SslLibraryBuildVersion: " << QSslSocket::sslLibraryBuildVersionString();
qDebug() << "SslLibraryRuntimeVersion: " << QSslSocket::sslLibraryVersionString();
You should install and put to your release the most similar to build version.
I had a shiny app that was deploying without problems on beta.rstudioconnect.com. I added some maps to it and then could no longer get it to work; one of the packages did not appear to be supported. I thought I might be able to get around this by using packrat on my project before deploying. However that didn't work. Now I can't seem to go back to my original version and don't understand where the problem lies. Does any of the following make any sense to anyone? what do I have to do to get back to my original (working) shiny? I had to take some lines out of the output to fit it in here:
Preparing to deploy application...DONE
Uploading bundle for application: 2539...DONE
Deploying bundle: 5321 for application: 2539 ...
Bundle requested R version 3.3.2; using /opt/R/3.3.1/bin/R which has version 3.3.1
2017/02/19 12:05:49.268297412 # Validating R library read / write permissions --------------------------------
2017/02/19 12:05:49.297061610 # Validating packrat installation ----------------------------------------------
2017/02/19 12:05:49.297171083 Installed packrat SHA is: 00bce0ead9f58d31c29e65fb7b87858586356f15
2017/02/19 12:05:49.297294331 Packaged packrat SHA is: 00bce0ead9f58d31c29e65fb7b87858586356f15
2017/02/19 12:05:49.298977087 Packrat is up-to-date.
2017/02/19 12:05:49.299134572 R version: 3.3.1
2017/02/19 12:05:49.299203258 packrat version: 0.4.8.11
2017/02/19 12:05:49.299948491 # Validating packrat cache read / write permissions ----------------------------
2017/02/19 12:05:49.494836685 Audited package hashes with local packrat installation.
2017/02/19 12:05:49.498803369 # Installing required R packages with `packrat::restore()` ---------------------
2017/02/19 12:05:51.169831244 Installing BH (1.62.0-1) ...
2017/02/19 12:05:51.182200494 Using cached BH.
2017/02/19 12:05:51.182461055 OK (symlinked cache)
2017/02/19 12:05:51.182679371 Installing DBI (0.5-1) ...
17/02/19 12:05:51.584223157 Installing packrat (0.4.8-1) ...
2017/02/19 12:05:51.595465126 Using cached packrat.
2017/02/19 12:05:51.595776430 OK (symlinked cache)
...
2017/02/19 12:05:52.163895821 Installing maptools (0.8-39) ...
2017/02/19 12:05:52.178467525 Using cached maptools.
2017/02/19 12:05:52.178690072 OK (symlinked cache)
2017/02/19 12:05:52.178939945 Installing dplyr (0.5.0) ...
2017/02/19 12:05:52.200480032 Using cached dplyr.
2017/02/19 12:05:52.200709370 OK (symlinked cache)
2017/02/19 12:05:52.200956042 Installing feather (0.3.1) ...
2017/02/19 12:06:05.282400309 [1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/opt/R/3.3.1/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmpssUwbS/feather' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package 'feather' ...\n** package 'feather' successfully unpacked and MD5 sums checked\nPlatform is little endian. Good.\n** libs\ng++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include\" -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o\ng++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include\" -fpic -g -O2 -c feather-read.cpp -o feather-read.o\ng++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include... <truncated>
t/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include\" -fpic -g -O2 -c feather-types.cpp -o feather-types.o\ng++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include\" -fpic -g -O2 -c feather-write.cpp -o feather-write.o\nIn file included from feather/api.h:24:0,\n from feather-read.cpp:4:\n./feather/common.h:24:28: error: both 'const' and 'constexpr' cannot be used here\n./feather/common.h:25:28: error: both 'const' and 'constexpr' cannot be used here\nIn file included from feather/api.h:25:0,\n from feather-read.cpp:4:\n./feather/io.h:73:29: error: expected ';' at end of member declaration\n./feather/io.h:73:35: error: 'override' does not name a type\n./feather/io.h:74:26: error: expected ';' at end of member declaration\n./feather/io.h:74:28: error: 'override' does not name a type\n./feather/io.h:75:59: error: expected ';' at end of m... <truncated>
ther/io.h:75:61: error: 'override' does not name a type\n./feather/io.h:93:29: error: expected ';' at end of member declaration\n./feather/io.h:93:35: error: 'override' does not name a type\n./feather/io.h:94:26: error: expected ';' at end of member declaration\n./feather/io.h:94:28: error: 'override' does not name a type\n./feather/io.h:95:59: error: expected ';' at end of member declaration\n./feather/io.h:95:61: error: 'override' does not name a type\n./feather/io.h:108:29: error: expected ';' at end of member declaration\n./feather/io.h:108:35: error: 'override' does not name a type\n./feather/io.h:109:26: error: expected ';' at end of member declaration\n./feather/io.h:109:28: error: 'override' does not name a type\n./feather/io.h:110:59: error: expected ';' at end of member declaration\n./feather/io.h:110:61: error: 'override' does not name a type\n./feather/io.h:150:16: error: expected ';' at end of member declaration\n./feather/io.h:150:18: error: 'override' does not name a typ... <truncated>
: error: expected ';' at end of member declaration\n./feather/io.h:151:35: error: 'override' does not name a type\n./feather/io.h:152:51: error: expected ';' at end of member declaration\n./feather/io.h:152:53: error: 'override' does not name a type\n./feather/io.h:172:16: error: expected ';' at end of member declaration\n./feather/io.h:172:18: error: 'override' does not name a type\n./feather/io.h:173:29: error: expected ';' at end of member declaration\n./feather/io.h:173:35: error: 'override' does not name a type\n./feather/io.h:174:51: error: expected ';' at end of member declaration\n./feather/io.h:174:53: error: 'override' does not name a type\nIn file included from feather/api.h:24:0,\n from feather-types.h:2,\n from feather-types.cpp:4:\n./feather/common.h:24:28: error: both 'const' and 'constexpr' cannot be used here\n./feather/common.h:25:28: error: both 'const' and 'constexpr' cannot be used here\nIn file included from feather/api.h:25:0,\n ... <truncated>
er-types.h:2,\n from feather-types.cpp:4:\n./feather/io.h:73:29: error: expected ';' at end of member declaration\n./feather/io.h:73:35: error: 'override' does not name a type\n./feather/io.h:74:26: error: expected ';' at end of member declaration\n./feather/io.h:74:28: error: 'override' does not name a type\n./feather/io.h:75:59: error: expected ';' at end of member declaration\n./feather/io.h:75:61: error: 'override' does not name a type\n./feather/io.h:93:29: error: expected ';' at end of member declaration\n./feather/io.h:93:35: error: 'override' does not name a type\n./feather/io.h:94:26: error: expected ';' at end of member declaration\n./feather/io.h:94:28: error: 'override' does not name a type\n./feather/io.h:95:59: error: expected ';' at end of member declaration\n./feather/io.h:95:61: error: 'override' does not name a type\n./feather/io.h:108:29: error: expected ';' at end of member declaration\n./feather/io.h:108:35: error: 'override' does not name a type\n.... <truncated>
ror: expected ';' at end of member declaration\n./feather/io.h:109:28: error: 'override' does not name a type\n./feather/io.h:110:59: error: expected ';' at end of member declaration\n./feather/io.h:110:61: error: 'override' does not name a type\n./feather/io.h:150:16: error: expected ';' at end of member declaration\n./feather/io.h:150:18: error: 'override' does not name a type\n./feather/io.h:151:29: error: expected ';' at end of member declaration\n./feather/io.h:151:35: error: 'override' does not name a type\n./feather/io.h:152:51: error: expected ';' at end of member declaration\n./feather/io.h:152:53: error: 'override' does not name a type\n./feather/io.h:172:16: error: expected ';' at end of member declaration\n./feather/io.h:172:18: error: 'override' does not name a type\n./feather/io.h:173:29: error: expected ';' at end of member declaration\n./feather/io.h:173:35: error: 'override' does not name a type\n./feather/io.h:174:51: error: expected ';' at end of member declaration\n... <truncated>
rror: 'override' does not name a type\nIn file included from feather/api.h:24:0,\n from feather_types.h:2,\n from RcppExports.cpp:4:\n./feather/common.h:24:28: error: both 'const' and 'constexpr' cannot be used here\n./feather/common.h:25:28: error: both 'const' and 'constexpr' cannot be used here\nIn file included from feather/api.h:25:0,\n from feather_types.h:2,\n from RcppExports.cpp:4:\n./feather/io.h:73:29: error: expected ';' at end of member declaration\n./feather/io.h:73:35: error: 'override' does not name a type\n./feather/io.h:74:26: error: expected ';' at end of member declaration\n./feather/io.h:74:28: error: 'override' does not name a type\n./feather/io.h:75:59: error: expected ';' at end of member declaration\n./feather/io.h:75:61: error: 'override' does not name a type\n./feather/io.h:93:29: error: expected ';' at end of member declaration\n./feather/io.h:93:35: error: 'override' does not name a type\n./fea... <truncated>
expected ';' at end of member declaration\n./feather/io.h:94:28: error: 'override' does not name a type\n./feather/io.h:95:59: error: expected ';' at end of member declaration\n./feather/io.h:95:61: error: 'override' does not name a type\n./feather/io.h:108:29: error: expected ';' at end of member declaration\n./feather/io.h:108:35: error: 'override' does not name a type\n./feather/io.h:109:26: error: expected ';' at end of member declaration\n./feather/io.h:109:28: error: 'override' does not name a type\n./feather/io.h:110:59: error: expected ';' at end of member declaration\n./feather/io.h:110:61: error: 'override' does not name a type\n./feather/io.h:150:16: error: expected ';' at end of member declaration\n./feather/io.h:150:18: error: 'override' does not name a type\n./feather/io.h:151:29: error: expected ';' at end of member declaration\n./feather/io.h:151:35: error: 'override' does not name a type\n./feather/io.h:152:51: error: expected ';' at end of member declaration\n./feathe... <truncated>
verride' does not name a type\n./feather/io.h:172:16: error: expected ';' at end of member declaration\n./feather/io.h:172:18: error: 'override' does not name a type\n./feather/io.h:173:29: error: expected ';' at end of member declaration\n./feather/io.h:173:35: error: 'override' does not name a type\n./feather/io.h:174:51: error: expected ';' at end of member declaration\n./feather/io.h:174:53: error: 'override' does not name a type\nIn file included from feather/api.h:24:0,\n from feather-write.cpp:4:\n./feather/common.h:24:28: error: both 'const' and 'constexpr' cannot be used here\n./feather/common.h:25:28: error: both 'const' and 'constexpr' cannot be used here\nIn file included from feather/api.h:25:0,\n from feather-write.cpp:4:\n./feather/io.h:73:29: error: expected ';' at end of member declaration\n./feather/io.h:73:35: error: 'override' does not name a type\n./feather/io.h:74:26: error: expected ';' at end of member declaration\n./feather/io.h:... <truncated>
does not name a type\n./feather/io.h:75:59: error: expected ';' at end of member declaration\n./feather/io.h:75:61: error: 'override' does not name a type\n./feather/io.h:93:29: error: expected ';' at end of member declaration\n./feather/io.h:93:35: error: 'override' does not name a type\n./feather/io.h:94:26: error: expected ';' at end of member declaration\n./feather/io.h:94:28: error: 'override' does not name a type\n./feather/io.h:95:59: error: expected ';' at end of member declaration\n./feather/io.h:95:61: error: 'override' does not name a type\n./feather/io.h:108:29: error: expected ';' at end of member declaration\n./feather/io.h:108:35: error: 'override' does not name a type\n./feather/io.h:109:26: error: expected ';' at end of member declaration\n./feather/io.h:109:28: error: 'override' does not name a type\n./feather/io.h:110:59: error: expected ';' at end of member declaration\n./feather/io.h:110:61: error: 'override' does not name a type\n./feather/io.h:150:16: error: exp... <truncated>
er declaration\n./feather/io.h:150:18: error: 'override' does not name a type\n./feather/io.h:151:29: error: expected ';' at end of member declaration\n./feather/io.h:151:35: error: 'override' does not name a type\n./feather/io.h:152:51: error: expected ';' at end of member declaration\n./feather/io.h:152:53: error: 'override' does not name a type\n./feather/io.h:172:16: error: expected ';' at end of member declaration\n./feather/io.h:172:18: error: 'override' does not name a type\n./feather/io.h:173:29: error: expected ';' at end of member declaration\n./feather/io.h:173:35: error: 'override' does not name a type\n./feather/io.h:174:51: error: expected ';' at end of member declaration\n./feather/io.h:174:53: error: 'override' does not name a type\nmake: *** [feather-types.o] Error 1\nmake: *** Waiting for unfinished jobs....\nmake: *** [feather-read.o] Error 1\nmake: *** [RcppExports.o] Error 1\nmake: *** [feather-write.o] Error 1\nERROR: compilation failed for package 'feather'\n* re... <truncated>
nect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/feather'"
2017/02/19 12:06:05.283810404 Error: Command failed (1)
2017/02/19 12:06:05.283822886
2017/02/19 12:06:05.283836187 Failed to run system command:
2017/02/19 12:06:05.283839368
2017/02/19 12:06:05.283847263 '/opt/R/3.3.1/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmpssUwbS/feather' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1' --install-tests --no-docs --no-multiarch --no-demo
2017/02/19 12:06:05.283878906
2017/02/19 12:06:05.283889984 The command failed with output:
2017/02/19 12:06:05.283899167 * installing *source* package 'feather' ...
2017/02/19 12:06:05.283908105 ** package 'feather' successfully unpacked and MD5 sums checked
2017/02/19 12:06:05.283911064 Platform is little endian. Good.
2017/02/19 12:06:05.283918990 ** libs
2017/02/19 12:06:05.283921520 g++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include" -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
2017/02/19 12:06:05.283944289 g++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include" -fpic -g -O2 -c feather-read.cpp -o feather-read.o
2017/02/19 12:06:05.283947838 g++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include" -fpic -g -O2 -c feather-types.cpp -o feather-types.o
2017/02/19 12:06:05.283955637 g++ -std=c++0x -I/opt/R/3.3.1/lib/R/include -DNDEBUG -I. -I/usr/local/include -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.3.1/Rcpp/include" -fpic -g -O2 -c feather-write.cpp -o feather-write.o
2017/02/19 12:06:05.283958522 In file included from feather/api.h:24:0,
2017/02/19 12:06:05.283967685 from feather-read.cpp:4:
2017/02/19 12:06:05.283970576 ./feather/common.h:24:28: error: both 'const' and 'constexpr' cannot be used here
2017/02/19 12:06:05.283978363 ./feather/common.h:25:28: error: both 'const' and 'constexpr' cannot be used here
2017/02/19 12:06:05.283981078 In file included from feather/api.h:25:0,
2017/02/19 12:06:05.283989020 from feather-read.cpp:4:
2017/02/19 12:06:05.283991718 ./feather/io.h:73:29: error: expected ';' at end of member declaration
2017/02/19 12:06:05.283999364 ./feather/io.h:73:35: error: 'override' does not name a type
2017/02/19 12:06:05.284001824 ./feather/io.h:74:26: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284162768 ./feather/io.h:172:18: error: 'override' does not name a type
2017/02/19 12:06:05.284165214 ./feather/io.h:173:29: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284171921 ./feather/io.h:173:35: error: 'override' does not name a type
2017/02/19 12:06:05.307706691 Warning message:
2017/02/19 12:06:05.307863198 In packrat::restore(overwrite.dirty = TRUE, prompt = FALSE, restart = FALSE) :
2017/02/19 12:06:05.307879290 The most recent snapshot was generated using R version 3.3.2
2017/02/19 12:06:05.284174366 ./feather/io.h:174:51: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284235118 ./feather/io.h:174:53: error: 'override' does not name a type
2017/02/19 12:06:05.284239266 In file included from feather/api.h:24:0,
2017/02/19 12:06:05.284246654 from feather-types.h:2,
2017/02/19 12:06:05.284249805 from feather-types.cpp:4:
2017/02/19 12:06:05.284256762 ./feather/common.h:24:28: error: both 'const' and 'constexpr' cannot be used here
2017/02/19 12:06:05.284259715 ./feather/common.h:25:28: error: both 'const' and 'constexpr' cannot be used here
2017/02/19 12:06:05.284266625 In file included from feather/api.h:25:0,
2017/02/19 12:06:05.284268985 from feather-types.h:2,
2017/02/19 12:06:05.284275396 from feather-types.cpp:4:
2017/02/19 12:06:05.284277912 ./feather/io.h:73:29: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284302465 ./feather/io.h:73:35: error: 'override' does not name a type
2017/02/19 12:06:05.284310963 ./feather/io.h:74:26: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284455903 ./feather/io.h:152:53: error: 'override' does not name a type
2017/02/19 12:06:05.284458901 ./feather/io.h:172:16: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284465785 ./feather/io.h:172:18: error: 'override' does not name a type
2017/02/19 12:06:05.284468388 ./feather/io.h:173:29: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284475582 ./feather/io.h:173:35: error: 'override' does not name a type
2017/02/19 12:06:05.284478069 ./feather/io.h:174:51: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284499196 ./feather/io.h:174:53: error: 'override' does not name a type
2017/02/19 12:06:05.284502459 In file included from feather/api.h:24:0,
2017/02/19 12:06:05.284510402 from feather_types.h:2,
2017/02/19 12:06:05.284520035 from RcppExports.cpp:4:
2017/02/19 12:06:05.284528059 ./feather/common.h:24:28: error: both 'const' and 'constexpr' cannot be used here
2017/02/19 12:06:05.284530517 ./feather/common.h:25:28: error: both 'const' and 'constexpr' cannot be used here
2017/02/19 12:06:05.284537373 In file included from feather/api.h:25:0,
2017/02/19 12:06:05.284539717 from feather_types.h:2,
2017/02/19 12:06:05.284546913 from RcppExports.cpp:4:
2017/02/19 12:06:05.284549095 ./feather/io.h:73:29: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284555829 ./feather/io.h:73:35: error: 'override' does not name a type
2017/02/19 12:06:05.284558295 ./feather/io.h:74:26: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284565421 ./feather/io.h:74:28: error: 'override' does not name a type
2017/02/19 12:06:05.284568368 ./feather/io.h:75:59: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284699666 ./feather/io.h:152:53: error: 'override' does not name a type
2017/02/19 12:06:05.284702743 ./feather/io.h:172:16: error: expected ';' at end of member declaration
2017/02/19 12:06:05.284709426 ./feather/io.h:172:18: error: 'override' does not name a typ
2017/02/19 12:06:05.284716004
2017/02/19 12:06:05.284724049 Unable to fully restore the R packages associated with this deployment.
2017/02/19 12:06:05.284726910 Please review the preceding messages to determine which package
2017/02/19 12:06:05.284734403 encountered installation difficulty and the cause of the failure.
2017/02/19 12:06:05.284737341
2017/02/19 12:06:05.284755686 Some typical reasons for package installation failures:
2017/02/19 12:06:05.284759213 * A system library needed by the R package is not installed.
2017/02/19 12:06:05.284766893 Some of the most common package dependencies are cataloged at:
2017/02/19 12:06:05.284769816 https://github.com/rstudio/shinyapps-package-dependencies
2017/02/19 12:06:05.284777079
2017/02/19 12:06:05.284779889 * The R package requires a newer version of R.
2017/02/19 12:06:05.284795781
2017/02/19 12:06:05.284799144 * The C/C++ compiler is outdated. This is often true for packages
2017/02/19 12:06:05.284806731 needing C++11 features.
2017/02/19 12:06:05.284810026
2017/02/19 12:06:05.284817282 * The R package is Windows-only or otherwise unavailable for this
2017/02/19 12:06:05.284820216 operating system.
2017/02/19 12:06:05.284827881
2017/02/19 12:06:05.284830674 * The package is housed in a private repository that requires
2017/02/19 12:06:05.284837746 authentication to access. For more details on this, see:
2017/02/19 12:06:05.284840342 http://docs.rstudio.com/connect/admin/process-management.html#private-packages
2017/02/19 12:06:05.284848534
2017/02/19 12:06:05.284851222 The package description and documentation will list system requirements
2017/02/19 12:06:05.284858379 and restrictions.
2017/02/19 12:06:05.284861051
2017/02/19 12:06:05.284883420 Please contact your RStudio Connect administrator for further help
2017/02/19 12:06:05.284887648 resolving this issue.
Application deployment failed with error: exit status 1\
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)
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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)
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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)
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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?