env: centos7
install curl
when i start install curl and ./configure --with-ssl --with-zlib, i occurs errors about libs, what mean about link-time? it's env set? i have no any experience about installtaion by make, needed to install other package? how to fix it?
./configrue --with-ssl --with-zlib
accurs errors:
checking run-time libs availability... failed
configure: error: one or more libs available at link-time are not available
run-time. Libs used at link-time: -lssh2 -lssl -lcrypto -lz
the errors occur bebause of openssl install
after installed openssl, should check up while it usefully
when i input openssl version, it show same unkown path errors
so, u should set:
ln -s /usr/local/lib64/libssl.so.1.1 /usr/lib64/libssl.so.1.1
ln -s /usr/local/lib64/libcrypto.so.1.1 /usr/lib64/libcrypto.so.1.1
it worked!
You can also add LD_LIBRARY_PATH in front of the configure script:
LD_LIBRARY_PATH=/usr/local/lib64 ./configure --with-ssl --with-zlib
Related
I have a compiled local install of GMP:
/path/to/gmp
.../lib/gmp.h
.../include/[gmp_binaries.etc]
Now, I export the path, just to test the install; I'll add symlinks in some central location once I get it working:
export LD_LIBRARY_PATH=/path/to/gmp:$LD_LIBRARY_PATH
g++ -lgmp
// error: /usr/bin/ld: cannot find -lgmp
export LD_LIBRARY_PATH=/path/to/gmp/include:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/path/to/gmp/lib:$LD_LIBRARY_PATH
g++ -lgmp
// error: /usr/bin/ld: cannot find -lgmp
Basically, my question is: how do I connect my local libraries to ld?
(And the point is installing content without sudo, so I can't "just ____," for the most part)
-l requires a -L location to search in g++. Make does not follow your LD_LIBRARY_PATH. Make needs a specific location to search for specific libraries not included in /usr/lib
# define library paths in addition to /usr/lib
# if I wanted to include libraries not in /usr/lib I'd specify
# their path using -Lpath, something like:
LFLAGS = -L/home/newhall/lib -L../lib
From this site
Find your libgmp file, and link as follows:
g++ -L/path/to/libgmp/ -lgmp
My ultimate goal is to get python package graph_tool working on my system and also on ipynb if possible. I have already brew install graph-tool, as indicated here, but that's still insufficient.
So I follow Anaconda instructions here, and I make decent progress, until the CGAL Library could not be found.
Note: to comply with the Anaconda instructions, I installed anaconda3 and created a new conda environment (named py36env) to conda install all the required packages (packages that must also match with python 3.6)
The entire ./configure output. Below is a snippet:
(py36env) $ ./configure --prefix=/Users/tamtran/anaconda3/envs/py36env/ --with-python-module-path=/Users/tamtran/anaconda3/envs/py36env/lib/python3.6/site-packages --with-cgal=/Users/tamtran/anaconda3/envs/py36env/
.
.
checking whether CGAL is available in /Users/tamtran/anaconda3/envs/py36env/... no
configure: error: CGAL library not found.
The entire config.log. Below is a snippet:
configure:21200: checking whether CGAL is available in /Users/tamtran/anaconda3/envs/py36env/
configure:21236: g++ -std=gnu++14 -o conftest -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 -DNDEBUG -I/Users/tamtran/anaconda3/envs/py36env//include -pthread -I/usr/local/include -L/Users/tamtran/anaconda3/envs/py36env//lib -lCGAL -lCGAL_Core -lgmp -lboost_thread-mt -lpthread conftest.cpp -lgmp -lgmp >&5
| #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
| #include <CGAL/convex_hull_2.h>
| typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
| CGAL::convex_hull_2(points.begin(),points.end(),std::back_inserter(result));
configure:21278: error: CGAL library not found.
CGAL_CPPFLAGS='-I/Users/tamtran/anaconda3/envs/py36env//include'
CGAL_FLAGS=''
CGAL_LDFLAGS='-L/Users/tamtran/anaconda3/envs/py36env//lib -lCGAL -lCGAL_Core -lgmp -lboost_thread-mt -lpthread'
Note: Even without the --with-cgal tag, the same issue occurs. It's also important (I think) that the CGAL search directory is within py36env because CGAL matching with python3.6 is in there, whereas CGAL-python3.5 is in conda root environment. The only differences of ./configure output without the CGAL directory are:
checking whether CGAL is available in /usr... no
checking whether CGAL is available in /usr/local... no
checking whether CGAL is available in /opt... no
checking whether CGAL is available in /opt/local... no
on mac os x You must use -lcgal (is using brew)
for example on fedora linux -lCGAL
I'm trying to install rJava on MacOS Sierra. Have to tried the tips and guides elsewhere for other other version MacOS such as https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X
and Install xlsx and rJava on Mac
but it does not work out. Much appreciate any help. Thanks.
My Mac version: macOS Sierra, version 10.12.15
My R version: 3.4.0 (2017-04-21)
My Rstudio version: Version 0.99.903
Java version:
bash-3.2$ /usr/libexec/java_home -V
bash-3.2$ java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)
bash-3.2$ R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.8.0_131
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on macOS
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -fPIC -Wall -g -O2 -c conftest.c -o conftest.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
override rw-r--r-- root/admin for /Library/Frameworks/R.framework/Resources/etc/Makeconf? (y/n [n]) n
not overwritten
override rw-r--r-- root/admin for /Library/Frameworks/R.framework/Resources/etc/ldpaths? (y/n [n]) n
not overwritten
Done.
When I tried to install rJava, I ran
`R --quiet -e 'install.packages("rJava", type="source", repos="http://cran.us.r-project.org")`
I got the errors:
clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
The downloaded source packages are in
‘/private/var/folders/w8/ksbj8dh15bz2lkss7h2tpzk80000gn/T/Rtmp6r9HI0/downloaded_packages’
Warning message:
In install.packages("rJava", type = "source", repos = "http://cran.us.r-project.org") :
installation of package ‘rJava’ had non-zero exit status
I ran:
"curl -#ROL https://www.rforge.net/rJava/snapshot/rJava_0.9-8.tar.gz
R CMD INSTALL rJava_0.9-8.tar.gz"
and got the following error messages:
clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
I dont know what to do. Thanks for your help.
This article here solved this fopenmp issue for me on macOS Sierra 10.12.4. I outlined the solution here but also below. The problem is that forenmp option is not supported in macOS gcc so we have to compile a new version of the gcc.
Solution to forenmp problem
I have tested this with Homerew's r-app brew cask install r-app and Oracle's JDK. Then I did the following
brew install homebrew/versions/gcc49 --without-multilib #Long ~70min compiling...
sudo chown -R $(whoami):admin /usr/local
brew link --overwrite --force gcc49
brew unlink gcc49 && brew link gcc49
brew install llvm
mkdir ~/.R; touch ~/.R/Makevars
echo "VER=-4.9
CC=gcc$(VER)
CXX=g++$(VER)
CXX1X=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/4.9.3/lib/gcc/4.9" > ~/.R/Makevars
and now
sudo R CMD javareconf
Rscript -e 'install.packages("rJava", repos="http://rforge.net", type="source")'
and now rJava is working!
Comments using OSX 10.12.6 with Java 1.8.0_181 and dealing with the above issue and another issue related to compiling rJava.
First:
Install rJava with these commands:
wget https://cran.r-project.org/src/contrib/rJava_0.9-10.tar.gz
tar xvfz rJava_0.9-10.tar.gz
cd rJava
R CMD INSTALL rJava
Why use R CMD INSTALL? This will keep the config.log file that will allow you to debug things; install.packages() does not and help you get might not be very helpful in that case (e.g. https://github.com/s-u/rJava/issues/111).
Second:
Make sure you run the following, if you've updated Java (remember you need the JDK, not JRE).
sudo R CMD javareconf
Error (checking JNI data types):
To fix this error:
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
do this:
sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
sudo ln -f -s /usr/local/lib/libjvm.dylib /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/
Error (unsupported option '-fopenmp):
To fix this error:
clang: error: unsupported option '-fopenmp
do the following:
Note: The instructions may need to be modified for newer versions of gcc, but make sure you get a version greater than 7 (see notes that follow); the following command can be used to find out the available versions:
brew search gcc
Then install gcc:
brew install gcc#7
sudo chown -R $(whoami):admin /usr/local
brew link --overwrite --force gcc#7
brew unlink gcc#7 && brew link gcc#7
brew install llvm
mkdir -p ~/.R
## Check the versions and folder in FLIBS match what you install
echo "CC=gcc-7
CXX=g++-7
CXX1X=g++-7
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc\#7/7.3.0/lib/gcc/7" > ~/.R/Makevars
Notes: You need any version of gcc greater than 7; the without-multilib flag mentioned in the earlier answer may not be available, but it is important. Why the without-multilib flag?: https://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/ and OpenMP/gcc on macOS : gcc --without-multilib not available
Then install rJava
R CMD INSTALL rJava
Finally, test library (you should see your Java version):
library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
Take a look here:
http://www.owsiak.org/?p=3671
You can find quite detailed description of how to deal with rJava in macOS.
Make sure to install JDK that is provided by Oracle before you proceed.
This is my compile command
gcc msg_utils.o -o mtm -lm -L/openssl-1.0.0a -lssl -lcrypto
I get error :
/usr/bin/ld: cannot find -lssl
Please tell me what wrong with my command ,the path to openssl is correct ,I get openssl source from :
https://www.openssl.org/source/openssl-1.0.0a.tar.gz
(I guess you are on Linux)
You should probably install some OpenSSL package in your Linux distribution.
Perhaps aptitude install libssl-dev on Debian related distributions.
If you compile OpenSSL from source code, you probably need some make install step and you might need to run ldconfig after that.
You might want to use pkg-config during compilation of your code:
gcc -Wall -g $(pkg-config -cflags openssl) \
msg_utils.o -o mtm \
$(pkg-config -libs openssl)
See also this and that
Trying to build mod_auth_openid on MountainLion with XCode Version 4.4.1 (4F1003), I get a complaint about a missing 'cc' command, as follows:
/usr/share/apr-1/build-1/libtool --silent --mode=link /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc -o mod_auth_openid.la -rpath /usr/libexec/apache2 -module -avoid-version libmodauthopenid.la -I/usr/include/apache2 -I/usr/include/apr-1 -I/usr/local/include -L/usr/local/lib -lopkele -lcurl -lexpat -ltidy -lssl -lcrypto -lz -L/usr/lib -lpcre -lcurl
/usr/share/apr-1/build-1/libtool: line 4574: /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc: No such file or directory
apxs:Error: Command failed with rc=8323072
What to do?
I faced a similar problem while trying to install mod_wsgi using homebrew on Mac (Mountain Lion).
Though bmargulies posted the answer in his comment by pointing to github link. But still posting the solution here for completeness.
Run the following command.
sudo ln -s /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain
And then re-run the install command
Ran into exactly this problem with Mountain Lion/Homebrew/mod_wsgi. The toolchain symlink did not solve the problem in my case. Went back to another Mac where I used MacPorts to do this with no issues and looked at the Portfile for mod_wsgi. They had a --disable-framework flag in the configure step. Added this flag and everything worked great. Details available in the gist here https://gist.github.com/talonsensei/6284446