I am unable to build sqlcipher on Windows with following these steps.
install Win32 OpenSSL v0.9.8m
install TclTk
rename MINGWPATH/bin/tclsh84.exe to tclsh.exe
cd sqlcipher
$ ./configure --disable-tcl --disable-amalgamation
CFLAGS="-DSQLITE_HAS_CODEC -I../OpenSSL/include /c/Windows/System32/libeay32.dll"
$ make
$ make dll
$ make install
At the link stage, gcc gives this error:
libtool: link: gcc -g -O2 -DSQLITE_OS_WIN=1 -I. -I./src -I./ext/rtree -D_HAVE_SQ
LITE_CONFIG_H -DBUILD_sqlite -DNDEBUG -DSQLITE_THREADSAFE=1 -DSQLITE_OMIT_LOAD_E
XTENSION=1 -DHAVE_READLINE=0 -o .libs/sqlite3.exe ./src/shell.c ./.libs/libsqli
te3.a -lpthread -L/usr/local/lib
./.libs/libsqlite3.a(func.o): In function `sqlite3RegisterBuiltinFunctions':
c:\sqlcipher/./src/func.c:1439: **undefined reference to `sqlcipher_exportFunc**'
collect2: ld çıkış durumu 1 ile döndü
make: *** [sqlite3.exe] Error 1
You forget to define SQLITE_TEMP_STORE as document has specified.
I can confirm it's working smoothly on Ubuntu 12.04 LTS , with latest source on github:
In short for dynamic linking:
./configure --enable-tempstore=yes CFLAGS="-DSQLITE_HAS_CODEC -DSQLITE_TEMP_STORE=2" LDFLAGS="-lcrypto"
Related
I've tried to solve this using the previous questions/answers on SO but without any success. So, here's my problem.
I'm using RStudio on and Ubuntu box (14.04) and I tried to upgrade rJava from sources and in the process I managed to lose it.
I tried to install it again using,
install.packages("rJava")
which returned the following error message,
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/darren/R/x86_64-pc-linux-gnu-library/3.2/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
So, I went to the terminal and typed,
sudo R CMD javareconf
which also gave the following error,
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
#include <jni.h>
^
compilation terminated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME : /usr/lib/jvm/default-java
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.
I tried to follow these links, one and two but they didn't seem to resolve my issue; there are more links on SO but I'm not sure which one to follow. I've also un-installed and re-installed RStudio via the Ubuntu Software Centre but this didn't make any difference.
Can anyone else help?
In short, I want to be able to use RStudio with rJava again without it destroying any other uses of Java (such as jmol).
You don't seem to have JDK installed. You will need at least
sudo apt-get install openjdk-7-jdk
then re-run
sudo R CMD javareconf
Make sure you do NOT set JAVA_HOME by hand - it will be detected automatically. You should then see something like this:
$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.7.0_91
Java home path : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags : -I$(JAVA_HOME)/../include
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
What is wrong with sudo apt-get install r-cran-rjava ?
See for example this earlier answer and the question / thread around it.
For an installation from scratch, you could still much worse than starting from sudo apt-get build-dep r-cran-rjava. It will get you the JDK corresponding to your Ubuntu version.
First i would recommend installing Rstudio from its website: https://www.rstudio.com/products/rstudio/download/ (i.e. Rstudio 64bit: https://download1.rstudio.org/rstudio-0.99.489-amd64.deb). This does not solve the problem directly, but it helps to avoid other bugs with Rstudio.
Regarding the error, trying to make sure you have JDK install. I don't think the command java -version can tell if JDK is installed. You have to check the package of JDK itself, or based on the error message, do this:
locate jni.h
The output should match or compatible with your JAVAHOME, e.g:
/usr/lib/jvm/java-7-openjdk-amd64/include/jni.h
/usr/lib/jvm/java-7-oracle/include/jni.h
Update 1:
R CMD javareconf is looking for the jni.h file under $(JAVA_HOME)/include
You have JDK installed, but it is very likely that you are having default java to a JRE directory, that why the error happened.
You can see where default-java is really pointing to by doing this command:
jRealDir=$(readlink -f /usr/lib/jvm/default-java)
echo $jRealDir
# sample correct output: /usr/lib/jvm/jdk1.8.0_65
# or /usr/lib/jvm/java-8-oracle if you default to Oracle's
# now check jni.h
ls -l $jRealDir/include/jni.h
# sample expected output:
# /usr/lib/jvm/jdk1.8.0_65/include/jni.h
If the ls command failed, you have to setup so that javareconf ( and later rJava) can use the java from JDK not from JRE. You have two options:
Method 1: Do it system-wide
This is convenient, but may effect other program like the one you mentioned jmol. But don't worry, this is revertible, just re-run the command and pick the old one. Do the following command and pick the dir that has JDK:
sudo update-alternatives --config java
After that test how jmol works, if it works alright then congrat. You are now ready to test rJava. If not, try the second method below
Method 2: Do it for R only
put this in the .Rprofile under your home directory
Sys.setenv(JAVA_HOME = '/usr/lib/jvm/jdk1.8.0_65')
# this set JAVA_HOME for R to correct java home dir.
After updating or creating the .Rprofile DO restart R in Rstudio. The R CMD javareconf may still fail in this case, but it should be OK if you run it from Shell under Tools menu of Rstudio.
Regarding the installing or Rstudio from Ubuntu's stock repo. It would not make a difference for getting rJava running. Then again, I recommend installing Rstudio for its homepage because new version also has some nice features (i.e. better autocompletion, which I like the most).
Here is link on R-Bloggers that worked for me: https://www.r-bloggers.com/installing-rjava-on-ubuntu/
sudo apt-get install -y default-jre
sudo apt-get install -y default-jdk
sudo R CMD javareconf
install.packages("rJava")
I've been dealing with this exact issue, nothing in this thread or other that are similar have solved it. I'm on Ubuntu 16.04, here's how I got it to work:
apt-get install openjdk-9-jdk
rm -rf /usr/lib/jvm/default-java
ln -s /usr/lib/jvm/java-9-openjdk-amd64/ /usr/lib/jvm/default-java
You can see where the JAVA_HOME is in the error message.
Then use locate jni.h to find where is jni.h, next use soft link to link this location to $(JAVA_HOME)/include, just like #biocyberman mentioned.
This is what I did:
ln -s /usr/lib/jvm/java-8-openjdk-amd64/include/jni.h /opt/conda/include/jni.h
ln -s /usr/lib/jvm/java-8-openjdk-amd64/include/linux/jni_md.h /opt/conda/include/jni_md.h
ln -s /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so /usr/lib/
Since my JAVA_HOME is /opt/conda and I also don't have jni_md.h and -ljvm.
I am use Ubuntu 16.04.
I am trying to compile the wkhtmltopdf with patched qt using these instructions and when i get to the make && make install it gives me an error has anyone else done this on Ubuntu 14.04? I can't figure out what to do from here.
these are the instructions i am following i know they are not for 14.04 but i hoped they would have worked https://gist.github.com/Zauberfisch/8773593
This is the error i get:
cd src/lib/ && make -f Makefile make[1]: Entering directory /temp/wkhtmltopdf/src/lib' rm -f libwkhtmltox.so.0.12.1 libwkhtmltox.so libwkhtmltox.so.0 libwkhtmltox.so.0.12 g++ -Wl,-O1 -Wl,-rpath,/temp/wkqt/lib -shared -Wl,-soname,libwkhtmltox.so.0 -o libwkhtmltox.so.0.12.1 ../../build/loadsettings.o ../../build/multipageloader.o ../../build/tempfile.o ../../build/converter.o ../../build/websettings.o ../../build/reflect.o ../../build/utilities.o ../../build/pdfsettings.o ../../build/pdfconverter.o ../../build/outline.o ../../build/tocstylesheet.o ../../build/imagesettings.o ../../build/imageconverter.o ../../build/pdf_c_bindings.o ../../build/image_c_bindings.o ../../build/moc_multipageloader_p.o ../../build/moc_converter_p.o ../../build/moc_pdfconverter_p.o ../../build/moc_imageconverter_p.o ../../build/moc_pdf_c_bindings_p.o ../../build/moc_image_c_bindings_p.o ../../build/moc_converter.o ../../build/moc_multipageloader.o ../../build/moc_utilities.o ../../build/moc_pdfconverter.o ../../build/moc_imageconverter.o ../../build/qrc_wkhtmltopdf.o -L/temp/wkqt/lib -lQtWebKit -lQtSvg -L/temp/wkqt/lib -L/usr/X11R6/lib -lQtXmlPatterns -lQtGui -lQtNetwork -lQtCore -lpthread /usr/bin/ld: ../../build/qrc_wkhtmltopdf.o: relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC ../../build/qrc_wkhtmltopdf.o: error adding symbols: Bad value collect2: error: ld returned 1 exit status make[1]: * [../../bin/libwkhtmltox.so.0.12.1] Error 1 make[1]: Leaving directory `/temp/wkhtmltopdf/src/lib' make: * [sub-src-lib-make_default-ordered] Error 2
I downloaded a binary from their site that already had the QT build and that fixed the issue for me. Thanks!
I cannot get Rcpp to work on Windows 8.1. When I run the following minimal example, I get an error.
> library(Rcpp)
> evalCpp("1 + 1")
g++ -m64 -I"C:/R/R-31~1.0/include" -DNDEBUG -I"C:/R/R-3.1.0/library/Rcpp/include" -
I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c file11dc2120723d.cpp -o
file11dc2120723d.o g++: not found make: *** [file11dc2120723d.o] Error 127 Warning message: running
command 'make -f "C:/R/R-31~1.0/etc/x64/Makeconf" -f "C:/R/R-31~1.0/share/make/winshlib.mk"
SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sourceCpp_97232.dll" WIN=64 TCLBIN=64
OBJECTS="file11dc2120723d.o"' had status 2
Error in sourceCpp(code = code, env = env, rebuild = rebuild, showOutput = showOutput, :
Error 1 occurred building shared library.
The two first entries in my path are:
PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;
R is installed in a directory C:\R\R-3.1.0
Rtools is in the directory C:\R\Rtools
Some additional information:
> library(devtools)
> find_rtools(T)
Scanning path...
ls : c:\Rtools\bin\ls.exe
Scanning registry...
Found c:/Rtools for 3.1
VERSION.txt
Rtools version 3.1.0.1942
[1] TRUE
> has_devel()
"C:/R/R-31~1.0/bin/x64/R" --vanilla CMD SHLIB foo.c
gcc -m64 -I"C:/R/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include"
O2 -Wall -std=gnu99 -mtune=core2 -c foo.c -o foo.o
gcc: not found
make: *** [foo.o] Error 127
Warning message:
running command 'make -f "C:/R/R-31~1.0/etc/x64/Makeconf" -f "C:/R/R-31~1.0/share/make/winshlib.mk"
SHLIB="foo.dll" WIN=64 TCLBIN=64 OBJECTS="foo.o"' had status 2
Error: Command failed (1)
> system('g++ -v')
Warning message:
running command 'g++ -v' had status 127
Unsure if you have solved your problem but it appears you don't have gcc or g++ installed. For windows you can get these tools with MinGW.
Install MinGW which you can donwload from here. The homepage for information is here
Once you have it installed MinGW, you can open the 'MinGW Installation Manager' and install the bin and dev for 'mingw32-gcc-g++'.
You must then update your PATH environmental variable to include 'C:\MinGW\bin' and 'C:\MinGW\msys\1.0\bin'.
Restart your R session, couldn't hurt to also reinstall 'Rcpp', and tryrequire(Rcpp); evalCpp("1 + 1") again.
I had this problem while trying to call C-code directly. Switching from the function system() to system2() solved it immediately.
I got that fix by installing RTools and adding RBuildTools to the path:
Sys.setenv("PATH" = paste(Sys.getenv("PATH"),
"C:\\RBuildTools\\3.4\\bin",
"C:\\RBuildTools\\3.4\\mingw_32",
"C:\\RBuildTools\\3.4\\mingw_64", sep = ";"))
I don't understand these things clearly but #cdeterman solutions was not working for building my package while its example evalCpp("1 + 1") did.
Hey I have seen the following two questions here:
Install Rmpi on Centos fails with "can't find -lmpi"
Installing Rmpi on LAM/MPI cluster
But they don't provide any concrete answer to the problem.
The following is some pertinent information:
R> system('echo "$LD_LIBRARY_PATH"')
/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib:/usr/lib64/openmpi/lib
R> install.packages("Rmpi", configure.args="--with-Rmpi-include=/usr/include/openmpi-x86_64 --with-Rmpi-libpath=/usr/lib64/openmpi --with-Rmpi-type=OPENMPI")
This is the last part of the error message:
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi -lmpi -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lmpi
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
Any help will be great. Thanks.
After installing openmpi-devel,
I see libmpi.so in /usr/lib64/openmpi/lib/.
$ sudo yum install openmpi-devel
$ sudo updatedb
$ locate libmpi.so
/usr/lib64/openmpi/lib/libmpi.so
/usr/lib64/openmpi/lib/libmpi.so.1
/usr/lib64/openmpi/lib/libmpi.so.1.0.2
The following should work:
install.packages(
"Rmpi",
configure.args = paste(
"--with-Rmpi-include=/usr/include/openmpi-x86_64",
"--with-Rmpi-libpath=/usr/lib64/openmpi/lib",
"--with-Rmpi-type=OPENMPI"
)
)
If may be necessary to tell the system to look for shared libraries in this directory, as well:
# echo "/usr/lib64/openmpi/lib" > /etc/ld.so.conf.d/openmpi.conf
# ldconfig
I am trying to install mySQL for Python on PPC ibook G4 running Leopard. I have Python 2.7.2, XCODE 3.1.3 and MAMP 1.9.6 installed.
I was trying both MySQL-Python-1.2.2 and MySQL-Python-1.2.3, but I am always getting this error:
andreass-ibook-g4:MySQL-python-1.2.3 aed0101$ sudo python setup.py buildrunning build
running build_py
copying MySQLdb/release.py -> build/lib.macosx-10.3-fat-2.7/MySQLdb
running build_ext
building '_mysql' extension
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -isysroot/Developer/SDKs/MacOSX10.4u.sdk -arch ppc -arch i386 -g -O2 -DNDEBUG -g -O3 -Dversion_info=(1,2,3,'final',0) -D__version__=1.2.3 -I/Applications/MAMP/Library/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.3-fat-2.7/_mysql.o -fno-omit-frame-pointer -g
_mysql.c:36:23: error: my_config.h: No such file or directory
_mysql.c:38:19: error: mysql.h: No such file or directory
_mysql.c:39:26: error: mysqld_error.h: No such file or directory
...more errors
lipo: can't figure out the architecture type of: /var/tmp//ccM5WtnK.out
error: command 'gcc-4.0' failed with exit status 1
Can anybody help me with this?
Thanks.
It looks like the MySQL development headers are not found. If running mysql_config from the shell gives an error, that's probably why. Make sure mysql_config is on your path or else edit site.cfg and set the correct path in there. Normally setup.py will bail out if mysql_config exits with an error, so it's not clear what happened here.