Shiny: Shiny won't load / install after httpuv install (tried solution in #2030 but did not work)

Created on 10 May 2018 · 8Comments · Source: rstudio/shiny

Hello

After an httpuv update, Shiny apps don't run because shiny library fails to load.
A rapid googling led me here :
https://github.com/rstudio/shiny/issues/2030

So I :

restarted R, went fine
reinstalled httpuv, went fine (after quite a long compilation and some warning messages about deprecating issues)
reinstalled shiny, crashed
run a sessioninfo::session_info()
- copy paste the entire console (all above steps) in this message

Plz, help... that shiny app is supposed to be a demo to show how great it is :-(
Also, sorry, but my R install is in French, although I hope most messages remain quite understandable do not hesitate to ask me for a translation if needed

Sylvain

Restarting R session...

R> install.packages("httpuv")
Installing package into ‘/home/alfred/R_libs’
(as ‘lib’ is unspecified)
essai de l'URL 'https://cran.rstudio.com/src/contrib/httpuv_1.4.3.tar.gz'

Content type 'application/x-gzip' length 1673359 bytes (1.6 MB)

downloaded 1.6 MB

installing source package ‘httpuv’ ...
* package ‘httpuv’ correctement décompressé et sommes MD5 vérifiées
* libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports-legacy.cpp -o RcppExports-legacy.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from RcppExports-legacy.cpp:23:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from RcppExports.cpp:4:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callback.cpp -o callback.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from /home/alfred/R_libs/later/include/later.h:6,
from /home/alfred/R_libs/later/include/later_api.h:4,
from callback.h:5,
from callback.cpp:1:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callbackqueue.cpp -o callbackqueue.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filedatasource-unix.cpp -o filedatasource-unix.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from uvutil.h:15,
from filedatasource.h:4,
from filedatasource-unix.cpp:3:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filedatasource-win.cpp -o filedatasource-win.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http.cpp -o http.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from webapplication.h:6,
from http.h:7,
from http.cpp:1:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c httprequest.cpp -o httprequest.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from /home/alfred/R_libs/later/include/later.h:6,
from /home/alfred/R_libs/later/include/later_api.h:4,
from httprequest.cpp:4:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c httpresponse.cpp -o httpresponse.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from uvutil.h:15,
from httpresponse.h:4,
from httpresponse.cpp:1:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c httpuv.cpp -o httpuv.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from uvutil.h:15,
from httpuv.cpp:12:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c set_invalid_parameter.c -o set_invalid_parameter.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c socket.cpp -o socket.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from webapplication.h:6,
from http.h:7,
from socket.h:4,
from socket.cpp:1:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c thread.cpp -o thread.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.cpp -o utils.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uvutil.cpp -o uvutil.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from uvutil.h:15,
from uvutil.cpp:1:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c webapplication.cpp -o webapplication.o
In file included from /home/alfred/R_libs/Rcpp/include/Rcpp/Module.h:338:0,
from /home/alfred/R_libs/Rcpp/include/Rcpp.h:64,
from httpuv.h:4,
from webapplication.cpp:2:
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
/home/alfred/R_libs/Rcpp/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){
^~~
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-base.cpp -o websockets-base.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-hixie76.cpp -o websockets-hixie76.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-hybi03.cpp -o websockets-hybi03.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-ietf.cpp -o websockets-ietf.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets.cpp -o websockets.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
(cd libuv \
&& touch aclocal.m4 \
&& touch -r aclocal.m4 configure Makefile.in \
&& CC="gcc -std=gnu99" CFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" ./configure "--quiet")
make --directory=libuv \
HAVE_DTRACE=0
make[1] : on entre dans le répertoire « /tmp/Rtmpx70QHv/R.INSTALL5c0a2609960f/httpuv/src/libuv »
CC src/libuv_la-fs-poll.lo
CC src/libuv_la-inet.lo
CC src/libuv_la-threadpool.lo
CC src/libuv_la-uv-common.lo
CC src/libuv_la-version.lo
CC src/unix/libuv_la-async.lo
CC src/unix/libuv_la-core.lo
CC src/unix/libuv_la-dl.lo
CC src/unix/libuv_la-fs.lo
CC src/unix/libuv_la-getaddrinfo.lo
CC src/unix/libuv_la-getnameinfo.lo
CC src/unix/libuv_la-loop-watcher.lo
CC src/unix/libuv_la-loop.lo
CC src/unix/libuv_la-pipe.lo
CC src/unix/libuv_la-poll.lo
CC src/unix/libuv_la-process.lo
CC src/unix/libuv_la-signal.lo
CC src/unix/libuv_la-stream.lo
CC src/unix/libuv_la-tcp.lo
CC src/unix/libuv_la-thread.lo
CC src/unix/libuv_la-timer.lo
CC src/unix/libuv_la-tty.lo
CC src/unix/libuv_la-udp.lo
CC src/unix/libuv_la-linux-core.lo
CC src/unix/libuv_la-linux-inotify.lo
CC src/unix/libuv_la-linux-syscalls.lo
CC src/unix/libuv_la-procfs-exepath.lo
CC src/unix/libuv_la-proctitle.lo
CC src/unix/libuv_la-sysinfo-loadavg.lo
CC src/unix/libuv_la-sysinfo-memory.lo
CCLD libuv.la
ar: u' modifier ignored sinceD' is the default (see `U')
make[1] : on quitte le répertoire « /tmp/Rtmpx70QHv/R.INSTALL5c0a2609960f/httpuv/src/libuv »
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http-parser/http_parser.c -o http-parser/http_parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1/sha1.c -o sha1/sha1.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -I"/home/alfred/R_libs/Rcpp/include" -I"/home/alfred/R_libs/BH/include" -I"/home/alfred/R_libs/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64/base64.cpp -o base64/base64.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o httpuv.so RcppExports-legacy.o RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o http.o httprequest.o httpresponse.o httpuv.o md5.o set_invalid_parameter.o socket.o thread.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o ./libuv/.libs/libuv.a ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -L/usr/lib/R/lib -lR
installing to /home/alfred/R_libs/httpuv/libs
* R
* demo
* preparing package for lazy loading
* help
* installing help indices
* building package indices
* testing if installed package can be loaded
DONE (httpuv)

The downloaded source packages are in
‘/tmp/Rtmp5BAP1W/downloaded_packages’
R> install.packages("shiny")
Installing package into ‘/home/alfred/R_libs’
(as ‘lib’ is unspecified)
essai de l'URL 'https://cran.rstudio.com/src/contrib/shiny_1.0.5.tar.gz'

Content type 'application/x-gzip' length 2330710 bytes (2.2 MB)

downloaded 2.2 MB

installing source package ‘shiny’ ...
* package ‘shiny’ correctement décompressé et sommes MD5 vérifiées
* R
* inst
* preparing package for lazy loading
* help
** installing help indices
* building package indices
* testing if installed package can be loaded
Error: package or namespace load failed for ‘shiny’:
.onLoad failed in loadNamespace() for 'shiny', details:
call: .Call("_httpuv_getRNGState", PACKAGE = "httpuv")
error: "_httpuv_getRNGState" non disponible pour .Call() pour le package"httpuv"
Erreur : le chargement a échoué
Exécution arrêtée
ERROR: loading failed
removing ‘/home/alfred/R_libs/shiny’
restoring previous ‘/home/alfred/R_libs/shiny’
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmp5BAP1W/downloaded_packages’
R> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.4.4 (2018-03-15)
os Ubuntu 18.04 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate fr_LU.UTF-8
tz Europe/Luxembourg
date 2018-05-10

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────
package * version date source
clisymbols 1.2.0 2017-05-21 CRAN (R 3.4.4)
sessioninfo 1.0.0 2017-06-21 CRAN (R 3.4.4)
withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
yaml 2.1.14 2016-11-12 CRAN (R 3.4.0)

Source

DrSylWil

Most helpful comment

Can you try the following?

install.packages("Rcpp")
install.packages("httpuv")
install.packages("shiny")

wch on 10 May 2018

👍3

All 8 comments

Can you try the following?

install.packages("Rcpp")
install.packages("httpuv")
install.packages("shiny")

wch on 10 May 2018

👍3

Another thought: It's possible there's another, older version of httpuv also installed on your system, but in a different directory. Can you run .libPaths() and the look in each of the listed directories for httpuv?

For example:

> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"      
[3] "/usr/lib/R/library"

In this case, you would check each of those directories for a subdirectory named httpuv. If you find them, can you provide the contents of the DESCRIPTION file in that directory? In the case above, there might be one at /usr/local/lib/R/site-library/httpuv/DESCRIPTION and /usr/local/R/library/httpuv/DESCRIPTION.

wch on 10 May 2018

👍1

Hello,

Thanks a lot for the help

Your first suggestion fixed the issue:
1- reinstall Rcpp
2- reinstall httpuv
3- reinstall shiny

shiny is now able to install, load, and my apps are working

I took a look also at my libPaths, and it turns out that I actually have two different versions of httpuv (1.4.3 and 1.3.5) in two different libPaths (the most recent in my personal path /home/alfer/R_libs, and the older one in a system path /usr/lib/R/site-library). Which is caused I guess by the fact that I installed some packages with sudo apt get, and some from within RStudio.

However, this conflict doesn't seem to prevent shiny to work (after the reinstall of Rcpp/httpuv/shiny). Might be because Rcpp was installed with sudo apt get, and following your advise I reinstalled it through RStudio.

But maybe it's safer to remove one of them? the oldest one I suppose.

I copy my Description files:

Thanks a lot !

"/home/alfred/R_libs"

Package: httpuv
Type: Package
Title: HTTP and WebSocket Server Library
Version: 1.4.3
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb],
Winston Chang [ctb]
Copyright: RStudio, Inc.; Joyent, Inc.; Nginx Inc.; Igor Sysoev; Niels
Provos; Internet Systems Consortium, Inc.; Alexander Chemeris
Maintainer: Joe Cheng joe@rstudio.com
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
License: GPL (>= 2) | file LICENSE
Depends: R (>= 2.15.1), methods
Imports: Rcpp (>= 0.11.0), utils, promises, later (>= 0.7.2)
LinkingTo: Rcpp, BH, later
URL: https://github.com/rstudio/httpuv
SystemRequirements: GNU make
RoxygenNote: 6.0.1.9000
Suggests: testthat, callr
NeedsCompilation: yes
Packaged: 2018-05-09 20:51:45 UTC; jcheng
Repository: CRAN
Date/Publication: 2018-05-10 13:55:00 UTC
Built: R 3.4.4; x86_64-pc-linux-gnu; 2018-05-10 20:05:21 UTC; unix

"/usr/lib/R/site-library"
Package: httpuv
Type: Package
Title: HTTP and WebSocket Server Library
Version: 1.3.5
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb],
Winston Chang [ctb]
Copyright: RStudio, Inc.; Joyent, Inc.; Nginx Inc.; Igor Sysoev; Niels
Provos; Internet Systems Consortium, Inc.; Alexander Chemeris
Maintainer: Joe Cheng joe@rstudio.com
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
License: GPL-3 | file LICENSE
Depends: R (>= 2.15.1), methods
Imports: Rcpp (>= 0.11.0), utils
LinkingTo: Rcpp
URL: https://github.com/rstudio/httpuv
SystemRequirements: GNU make
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-07-03 21:47:04 UTC; jcheng
Repository: CRAN
Date/Publication: 2017-07-04 07:02:15 UTC
Built: R 3.4.2; x86_64-pc-linux-gnu; 'Thu, 14 Sep 2017 13:36:54 +0200'; unix

DrSylWil on 10 May 2018

In my opinion, it's best to install packages at the user level, unless you have a specific reason to install them as root. When you have the same package installed in multiple levels of your libpath, things should generally work, but when they don't, it can make things harder to diagnose.

wch on 10 May 2018

Reinstalling Rcpp and then httpuv worked for me. Thanks! Reinstalling httpuv alone was not sufficient.

sjackman on 6 Jul 2018

I was doing a bit of RPM packaging, and got the same _httpuv_getRNGState problem. It turned out that httpuv was build with -fvisibility=hidden, but R_init_httpuv wasn't explicitly exported. I've solved this by patching in some visibility into src/RcppExports.cpp like this:

RcppExport void R_init_httpuv(DllInfo *dll) __attribute__((visibility("default")));

In a newer versions of Rcpp this is already done automatically by RcppExport macro above. Probably httpuv should put a stricter lower bound on Rcpp version.

binarin on 6 Nov 2018

When I published my first Shiny App to a remote R Server:

2019/04/23 14:42:54.687002238 Installing httpuv (1.5.1) ... 
# errored out with the following message:
<p id="message">database is locked</p>

I rebooted my R Connect Server (EC2 machine) and retried the publishing. This time it installed httpuv successfully.

ghost on 23 Apr 2019

try to update the package:
"htmltools"
this is how i fixed the issue

jonykoren on 23 Jul 2020

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