wch
commented
6 years ago Using Docker with Centos 6, I've been able to get a similar error.
Dockerfile:
FROM centos:centos6
RUN yum -y install epel-release
RUN yum -y update
RUN echo "LANG=en_US.utf8" >> /etc/locale.conf
RUN localedef -c -f UTF-8 -i en_US en_US.UTF-8
RUN export LC_ALL=en_US.UTF-8
RUN yum -y install libtool R-core R-core-devel R-java R-cpp openssl-devel libcurl-devel \
&& echo 'options(repos = c(CRAN = "https://cran.rstudio.com/"), download.file.method = "libcurl")' >> /usr/lib64/R/etc/Rprofile.site
# Create directories for documentation
RUN mkdir -p /usr/share/doc/R-3.4.3/html
RUN cp /usr/lib64/R/library/stats/html/R.css /usr/share/doc/R-3.4.3/html/
# First install devtools and CRAN version httpuv so that we have dependencies
RUN R -e "install.packages(c('devtools', 'httpuv'))"
CMD bashBuild the container, then build httpuv:
docker build -t centos6r .
docker run --rm -ti centos6r
R
devtools::install_github('rstudio/httpuv')The error I get is this:
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -fvisibility=hidden -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -I"/usr/lib64/R/library/later/include" -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 -c http.cpp -o http.o
In file included from websockets.h:11,
from webapplication.h:7,
from http.h:7,
from http.cpp:1:
utils.h: In function ‘void err_printf(const char*, ...)’:
utils.h:52: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result
In file included from http.cpp:2:
httprequest.h: In constructor ‘HttpRequest::HttpRequest(uv_loop_t*, boost::shared_ptr<WebApplication>, boost::shared_ptr<Socket>, CallbackQueue*)’:
httprequest.h:98: error: no matching function for call to ‘boost::shared_ptr<Rcpp::Environment_Impl<Rcpp::PreserveStorage> >::shared_ptr(NULL)’
/usr/lib64/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:634: note: candidates are: boost::shared_ptr<T>::shared_ptr(boost::shared_ptr<T>&&) [with T = Rcpp::Environment_Impl<Rcpp::PreserveStorage>]
/usr/lib64/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:422: note: boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = Rcpp::Environment_Impl<Rcpp::PreserveStorage>]
/usr/lib64/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:370: note: boost::shared_ptr<T>::shared_ptr(boost::detail::sp_internal_constructor_tag, typename boost::detail::sp_element<T>::type*, boost::detail::shared_count&&) [with T = Rcpp::Environment_Impl<Rcpp::PreserveStorage>]
/usr/lib64/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:364: note: boost::shared_ptr<T>::shared_ptr(boost::detail::sp_internal_constructor_tag, typename boost::detail::sp_element<T>::type*, const boost::detail::shared_count&) [with T = Rcpp::Environment_Impl<Rcpp::PreserveStorage>]
/usr/lib64/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:352: note: boost::shared_ptr<T>::shared_ptr() [with T = Rcpp::Environment_Impl<Rcpp::PreserveStorage>]
make: *** [http.o] Error 1
ERROR: compilation failed for package ‘httpuv’[root@0a0fa6f6d84e /]# g++ --version
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
blueagave
ivlachos
jcheng5
bioinfotec
Hello,
We're running into a uv.h issue when attempting to install httpuv for r-3.4.3 on a rhel6 host. Compiling with gcc-4.4.7. I would appreciate any suggestions you may have to offer.
..... In file included from ./libuv/include/uv.h:67, from uvutil.h:6, from filedatasource.h:4, from filedatasource-unix.cpp:3: ./libuv/include/uv-private/uv-unix.h:132: error: ‘sem_t’ does not name a type In file included from uvutil.h:6, from filedatasource.h:4, from filedatasource-unix.cpp:3: ./libuv/include/uv.h:1893: error: ‘uv_sem_t’ was not declared in this scope ./libuv/include/uv.h:1893: error: ‘sem’ was not declared in this scope ./libuv/include/uv.h:1893: error: expected primary-expression before ‘unsigned’ ./libuv/include/uv.h:1893: error: initializer expression list treated as compound expression ./libuv/include/uv.h:1894: error: variable or field ‘uv_sem_destroy’ declared void
Thanks, Tom