Just installed the iRuby kernel following the istructions but when i do jupyter-notebook command and start a new notebook kernel dies and there is a problem reported on the terminal about libczmq:
[I 18:05:11.900 NotebookApp] Kernel started: bcb56cdd-964a-4dae-8a40-76dbcbe7e418
WARNING: ::CZMQ::FFI is not available without libczmq.
Unable to load this gem. The libzmq library (or DLL) could not be found.
If this is a Windows platform, make sure libzmq.dll is on the PATH.
If the DLL was built with mingw, make sure the other two dependent DLLs,
libgcc_s_sjlj-1.dll and libstdc++6.dll, are also on the PATH.
For non-Windows platforms, make sure libzmq is located in this search path:
["/var/lib/gems/2.3.0/gems/ffi-rzmq-core-1.0.6/lib/ffi-rzmq-core/../../ext/libzmq.so", "/home/randomx/anaconda3/bin/libzmq.so", "/home/randomx/bin/libzmq.so", "/home/randomx/.local/bin/libzmq.so", "/usr/local/sbin/libzmq.so", "/usr/local/bin/libzmq.so", "/usr/sbin/libzmq.so", "/usr/bin/libzmq.so", "/sbin/libzmq.so", "/bin/libzmq.so", "/usr/games/libzmq.so", "/usr/local/games/libzmq.so", "/snap/bin/libzmq.so", "/usr/lib/libzmq.so", "/usr/local/lib/libzmq.so", "/opt/local/lib/libzmq.so", "/usr/lib64/libzmq.so"]
You should install cztop, rbczmq or ffi_rzmq before running iruby notebook. See README.
F, [2017-03-26T18:05:12.031981 #13088] FATAL -- : Kernel died: uninitialized constant IRuby::Kernel::Session
/var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/kernel.rb:18:in `initialize'
/var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/command.rb:70:in `new'
/var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/command.rb:70:in `run_kernel'
/var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/command.rb:34:in `run'
/var/lib/gems/2.3.0/gems/iruby-0.3/bin/iruby:5:in `<top (required)>'
/usr/local/bin/iruby:23:in `load'
/usr/local/bin/iruby:23:in `<main>'
/var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/kernel.rb:18:in `initialize': uninitialized constant IRuby::Kernel::Session (NameError)
from /var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/command.rb:70:in `new'
from /var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/command.rb:70:in `run_kernel'
from /var/lib/gems/2.3.0/gems/iruby-0.3/lib/iruby/command.rb:34:in `run'
from /var/lib/gems/2.3.0/gems/iruby-0.3/bin/iruby:5:in `<top (required)>'
from /usr/local/bin/iruby:23:in `load'
from /usr/local/bin/iruby:23:in `<main>'
[I 18:05:14.903 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING: ::CZMQ::FFI is not available without libczmq.
So I installed cztop and ffi_rzmq but when i go to install rbczmq I got an error install message like this:
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating src/libczmq.pc
config.status: creating addons/Makefile
config.status: creating src/platform.h
config.status: executing depfiles commands
config.status: executing libtool commands
"make all && make install"
Making all in src
make[1]: ingresso nella directory "/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/czmq/src"
make all-am
make[2]: ingresso nella directory "/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/czmq/src"
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zauth.lo -MD -MP -MF .deps/zauth.Tpo -c -o zauth.lo zauth.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zauth.lo -MD -MP -MF .deps/zauth.Tpo -c zauth.c -o zauth.o
mv -f .deps/zauth.Tpo .deps/zauth.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zbeacon.lo -MD -MP -MF .deps/zbeacon.Tpo -c -o zbeacon.lo zbeacon.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zbeacon.lo -MD -MP -MF .deps/zbeacon.Tpo -c zbeacon.c -o zbeacon.o
mv -f .deps/zbeacon.Tpo .deps/zbeacon.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zcert.lo -MD -MP -MF .deps/zcert.Tpo -c -o zcert.lo zcert.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zcert.lo -MD -MP -MF .deps/zcert.Tpo -c zcert.c -o zcert.o
mv -f .deps/zcert.Tpo .deps/zcert.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zcertstore.lo -MD -MP -MF .deps/zcertstore.Tpo -c -o zcertstore.lo zcertstore.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zcertstore.lo -MD -MP -MF .deps/zcertstore.Tpo -c zcertstore.c -o zcertstore.o
mv -f .deps/zcertstore.Tpo .deps/zcertstore.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zchunk.lo -MD -MP -MF .deps/zchunk.Tpo -c -o zchunk.lo zchunk.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zchunk.lo -MD -MP -MF .deps/zchunk.Tpo -c zchunk.c -o zchunk.o
mv -f .deps/zchunk.Tpo .deps/zchunk.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zclock.lo -MD -MP -MF .deps/zclock.Tpo -c -o zclock.lo zclock.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zclock.lo -MD -MP -MF .deps/zclock.Tpo -c zclock.c -o zclock.o
mv -f .deps/zclock.Tpo .deps/zclock.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zconfig.lo -MD -MP -MF .deps/zconfig.Tpo -c -o zconfig.lo zconfig.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zconfig.lo -MD -MP -MF .deps/zconfig.Tpo -c zconfig.c -o zconfig.o
mv -f .deps/zconfig.Tpo .deps/zconfig.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zctx.lo -MD -MP -MF .deps/zctx.Tpo -c -o zctx.lo zctx.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zctx.lo -MD -MP -MF .deps/zctx.Tpo -c zctx.c -o zctx.o
mv -f .deps/zctx.Tpo .deps/zctx.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zdir.lo -MD -MP -MF .deps/zdir.Tpo -c -o zdir.lo zdir.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../include -pedantic -Werror -Wall -D_GNU_SOURCE -DLINUX -D_REENTRANT -D_THREAD_SAFE -g -I/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/rbczmq/dst/include -g -fPIC -MT zdir.lo -MD -MP -MF .deps/zdir.Tpo -c zdir.c -o zdir.o
zdir.c: In function ‘zdir_new’:
zdir.c:156:9: error: ‘readdir_r’ is deprecated [-Werror=deprecated-declarations]
int rc = readdir_r (handle, entry, &result);
^~~
In file included from ../include/czmq_prelude.h:257:0,
from ../include/czmq.h:31,
from zdir.c:35:
/usr/include/dirent.h:183:12: note: declared here
extern int readdir_r (DIR *__restrict __dirp,
^~~~~~~~~
zdir.c:159:13: error: ‘readdir_r’ is deprecated [-Werror=deprecated-declarations]
rc = readdir_r (handle, entry, &result);
^~
In file included from ../include/czmq_prelude.h:257:0,
from ../include/czmq.h:31,
from zdir.c:35:
/usr/include/dirent.h:183:12: note: declared here
extern int readdir_r (DIR *__restrict __dirp,
^~~~~~~~~
cc1: all warnings being treated as errors
Makefile:774: set di istruzioni per l'obiettivo "zdir.lo" non riuscito
make[2]: *** [zdir.lo] Errore 1
make[2]: uscita dalla directory "/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/czmq/src"
Makefile:586: set di istruzioni per l'obiettivo "all" non riuscito
make[1]: *** [all] Errore 2
make[1]: uscita dalla directory "/var/lib/gems/2.3.0/gems/rbczmq-1.7.9/ext/czmq/src"
Makefile:414: set di istruzioni per l'obiettivo "all-recursive" non riuscito
make: *** [all-recursive] Errore 1
CZMQ compile error!
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.
Provided configuration options:
--with-opt-dir
--without-opt-dir
--with-opt-include
--without-opt-include=${opt-dir}/include
--with-opt-lib
--without-opt-lib=${opt-dir}/lib
--with-make-prog
--without-make-prog
--srcdir=.
--curdir
--ruby=/usr/bin/$(RUBY_BASE_NAME)2.3
--with-system-libs
--without-system-libs
--with-system-libs
--without-system-libs
extconf failed, exit code 1
I also have installed libtool autogen autoconf automake but installation fails anyway..I got the last version of Kubuntu as os
What can I do? Thank you for help
Solved! I had to install the zeromq source from here
http://zeromq.org/intro:get-the-software
n order to install caffe,which is used for deep learing,i need to upgrade gcc version from 4.4.7 to 4.8.2 in redhat 6.5。
First run ./configure it worked,
then make -j4, it will report
options.c:11145: error: narrowing conversion of '-0x00000000000000001' from 'int' to 'short unsigned int' inside { }
g++ -std=gnu++0x -c -g -DIN_GCC -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wwrite-strings -Wcast-qual -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common -DHAVE_CONFIG_H -I. -I. -I../../gcc -I../../gcc/. -I../../gcc/../include -I../../gcc/../libcpp/include -I../../gcc/../libdecnumber -I../../gcc/../libdecnumber/bid -I../libdecnumber -I../../gcc/../libbacktrace ../../gcc/hash-table.c -o hash-table.o
g++ -std=gnu++0x -c -g -DIN_GCC -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wwrite-strings -Wcast-qual -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common -DHAVE_CONFIG_H -I. -I. -I../../gcc -I../../gcc/. -I../../gcc/../include -I../../gcc/../libcpp/include -I../../gcc/../libdecnumber -I../../gcc/../libdecnumber/bid -I../libdecnumber -I../../gcc/../libbacktrace ../../gcc/file-find.c -o file-find.o
make[3]: *** [options.o] Error 1
make[3]: *** Waiting for unfinished jobs....
I search google,but can't find good ways to fix it ,who has the same issues before?
Replacing the original gcc can cause problems. The alternative is to install Developer Toolset which installs a new gcc version (currently at 4.9) along side the original to avoid file conflict. Get started here: http://developers.redhat.com/products/developertoolset/overview/
I am trying to compile pkcs11-helper under Cygwin with GCC. After configuring I called make. These are the last lines of its output:
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../include -I/usr/include -g -O2 -MT _pkcs11h-crypto-openssl.lo -MD -MP -MF .deps/_pkcs11h-crypto-openssl.Tpo -c -o _pkcs11h-crypto-openssl.lo _pkcs11h-crypto-openssl.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../include -I/usr/include -g -O2 -MT _pkcs11h-crypto-openssl.lo -MD -MP -MF .deps/_pkcs11h-crypto-openssl.Tpo -c _pkcs11h-crypto-openssl.c -DDLL_EXPORT -DPIC -o .libs/_pkcs11h-crypto-openssl.o
_pkcs11h-crypto-openssl.c:57:26: fatal error: openssl/x509.h: No such file or directory
Why doesn't GCC find my /usr/include/openssl/x509.h (which definitely exists)? As you can see I even passed -I/usr/include (there will be the same message without it).
This is the corresponding line 57 in _pkcs11h-crypto-openssl.c:
#include <openssl/x509.h>
My GNU scientific library (http://www.gnu.org/software/gsl/) installed in the path: /home/myname/gsl-1.6
My mlRho 1.7-stat prog (http://guanine.evolbio.mpg.de/mlRho/mlRho_1.7.tgz) which uses GNU scientific library-installed in:/home/myname/MlRho_1.7
my operating system: Fedora 16
original make file in mlRho
cd /home/myname/MlRho_1.7/
vim make
CC=gcc
CFLAGS= -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 \
-I/opt/local/include/ -L/opt/local/lib/
I have changed path in mlRho
CC=gcc
CFLAGS= -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 \
-I/home/myname/gsl-1.6 -L/home/myname/gsl-1.6
after making changes, I tried running make, it gives error
make
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/home/myname/gsl-1.6/include/ -L/home/myname/gsl-1.6/lib/ -c -o mlRho.o mlRho.c
In file included from mlRho.c:16:0:
mlComp.h:7:30: fatal error: gsl/gsl_sf_gamma.h: No such file or directory
compilation terminated.
make: *** [mlRho.o] Error 1
when i do make test- it gives me error below
make test
make[1]: Entering directory `/home/myname/MlRho_1.7/TestMlPi'
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o testMlPi.o testMlPi.c
testMlPi.c: In function ‘main’:
testMlPi.c:62:67: warning: variable ‘sderr’ set but not used [-Wunused-but-set-variable]
testMlPi.c:62:60: warning: variable ‘sdhet’ set but not used [-Wunused-but-set-variable]
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o interface.o interface.c
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o eprintf.o eprintf.c
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o ranNum.o ranNum.c
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -o testMlPi testMlPi.o interface.o eprintf.o ranNum.o -lm
make[1]: Leaving directory `/home/myname/MlRho_1.7/TestMlPi'
Output from testMlPi:
pi: 5.00e-05 epsilon: 4.90e-04 -log(L): 1.40e+05
Output from mlRho:
make: ./mlRho: Command not found
make: *** [testPi] Error 127
Output from mlRho:
make: ./mlRho: Command not found
make: *** [testPi] Error 127
It somehow GNU library not linking to mlRho programme. How to fix it?
yum installs GIMP 2.8 on Fedora 17, but I want to use 2.6 so I'm trying to compile it. However, I keep getting this error saying it can't find gegl.h, which is installed and on the include path:
[root#life gegl]# pwd
/home/james/packages/gimp-2.6.12/app/gegl
[root#life gegl]# make
gcc -DHAVE_CONFIG_H -I. -I../.. -I../.. -I../.. -I../../app -I../../app /usr/include/gegl-0.1/ -pthread -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng15 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/local/include -DG_LOG_DOMAIN=\"Gimp-GEGL\" -DGIMP_DISABLE_DEPRECATED -DGDK_MULTIHEAD_SAFE -DGTK_MULTIHEAD_SAFE -g -O2 -Wall -Wdeclaration-after-statement -Wmissing-prototypes -Wmissing-declarations -Winit-self -Wpointer-arith -Wold-style-definition -Wformat-security -MT gimp-gegl.o -MD -MP -MF .deps/gimp-gegl.Tpo -c -o gimp-gegl.o gimp-gegl.c
gimp-gegl.c:24:18: fatal error: gegl.h: No such file or directory
compilation terminated.
make: *** [gimp-gegl.o] Error 1
[root#life gegl]# ls -l /usr/include/gegl-0.1/gegl.h
-rw-r--r--. 1 root root 31086 Nov 18 2011 /usr/include/gegl-0.1/gegl.h
Please re-run config:
gcc -DHAVE_CONFIG_H
-I.
-I../..
-I../..
-I../..
-I../../app
-I../../app
/usr/include/gegl-0.1/ // THIS IS WRONG: it should be "-I/usr/include/gegl-0.1"
-pthread
...
Please also make sure your "-L" and/or "-l" library paths are correct at link time, too.