I am trying to compile Blochlibs-1.2 libraries on Ubuntu 15.04 (32 bit). Ihave successfully compiled fftw3 and mpi libraries which all ended up in /usr/local/lib and usr/local/include. mpicc is in the path and LD_LIBRARY_PATH is set correctly. when I run configure like this:
./configure --with-mpi=/usr/local --with-fftw=/usr/local
then i get this error:
checking for functioning MPI library ... configure: error: couldn't
find mpi library for --with-mpi
How does the configure file search for the libraries?
Thanks,
Z
Related
I'm using CMake as a build tool to create C++ shared library with Rcpp. To trigger CMake while invoking R CMD INSTALL command the top configure script need to look something like this:
rm -rf _builds
cmake -H. -B_builds
cmake --build _builds
...
Such approach works nicely on Linux and Mac OS, but not on Windows machine.
What version of CMake expected in configure:
windows native cmake
cygwin cmake
What generator do I need to use:
Unix Makefiles (cygwin)
MSYS Makefiles (native)
MinGW Makefiles (native)
SSCCE
https://github.com/forexample/rcpp-test
Leave all Makefile files (Makefile.win for windows) empty:
all:
Put CMake build instructions into configure (configure.win for windows):
cmake -H. -B_builds
cmake --build _builds
Such approach works nice for me on Linux, Mac and Windows (native cmake with Visual Studio generator). Note that it's probably not compatible with cran and windows build need to be tuned to compile different architectures (see R_ARCH) but it works locally and fit my needs.
Example
I'm new to native client. I'm trying to follow the official tutorial on my newly installed ubuntu 14.
I'm getting the following when running "make serve" under the getting_started folder. I googled, it seems to be related to 32/64 bit. my system is 64bit, but pnacl seems to think it is 32.
Anyway I couldn't find a solution. do you know how?
/media/shi/work/nacl_sdk/pepper_34/toolchain/linux_pnacl/bin/pnacl-clang++ -o hello_tutorial.bc hello_tutorial.cc -O2 -I/media/shi/work/nacl_sdk/pepper_34/include -L/media/shi/work/nacl_sdk/pepper_34/lib/pnacl/Release -lppapi_cpp -lppapi
/media/shi/work/nacl_sdk/pepper_34/toolchain/linux_pnacl/host_x86_32/bin/clang: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory
make[1]: * [hello_tutorial.bc] Error 127
make[1]: Leaving directory `/media/shi/work/nacl_sdk/pepper_34/getting_started/part1'
make: * [part1_ALL_TARGET] Error 2
It's probably easiest to install the i386 C/C++ libraries:
sudo apt-get install libc6:i386 libstdc++6:i386
There are 64-bit binaries included in the SDK as well (in toolchain/linux_pnacl/bin64/), but they are not run by default (and I'm not certain of an easy way to make the SDK use them).
I have download the Qt-everywhere-4.8.5.tar.gz from Qt official website. And In the CentOS 5.X, it's GCC version is 4.1.2. So I have compiled the gcc-4.7.2 from source code and installed it in $HOME/software/, then in the install directory, there are bin and lib and lib64, and I have add the path into LD_LIBRARY_PATH.
Then, I uncompressed the qt source code, configure it with
./configure -prefix $HOME/softwares/ -nomake demos -nomake examples
Then, make it. there is an error:
/home/user/Downloads/qt-everywhere-opensource-src-4.8.5/bin/lrelease:assistant_cs.ts -qm assistant_cs.qm
/home/user/Downloads/qt-everywhere-opensource-src-4.8.5/bin/lrelease: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/user/Downloads/qt-everywhere-opensource-src-4.8.5/bin/lrelease)
/home/user/Downloads/qt-everywhere-opensource-src-4.8.5/bin/lrelease: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /home/user/Downloads/qt-everywhere-opensource-src-4.8.5/bin/lrelease)
gmake[1]: *** [assistant_cs.qm] Error 1
And, I have found the libstdc++.so.6 in $HOME/softwares/lib64, and I have add the path into LD_LIBRARY_PATH, why the make command just use the system's library, not use the provided one? I have no root privileges, so I can't link the system's library with my home gcc's library. Could you give me some advice, please? Thanks.
I'm trying to configure my Qt for Embedded Linux with a virtual framebuffer according to these instructions. From the Qt for Embedded source folder, I'm trying:
./configure -embedded -opensource -confirm-license -verbose -qvfb
make
I get the following error which prevents me from doing make install:
.obj/release-shared-emb-x86/qtextcodec.o: In function `setup()':
qtextcodec.cpp:(.text+0x23cc): undefined reference to `QIconvCodec::QIconvCodec()'
collect2: ld returned 1 exit status
make[1]: *** [../../lib/libQtCore.so.4.8.4] Error 1
make[1]: Leaving directory `/home/cstjean/qt/src/corelib'
make: *** [sub-corelib-all-ordered] Error 2
If I do:
./configure -embedded -opensource -confirm-license -verbose -qvfb
make -no-iconv
sudo make install -no-iconv
...This works. But when I go into QtCreator, Tools > Options > Build & Run > Qt Versions, I try to select qmake for Qt Embedded (for me it's in /home/cstjean/qt/bin/qmake) and it tells me:
Qt version is not properly installed, please run make install
I've tried googling this like crazy. There are a lot of suggestions to download various libraries, which I've tried to no avail, but perhaps I'm missing something because this is a pretty fresh installation of Ubuntu I'm using.
Thanks.
I solved this problem by installing Gnome and starting over from scratch for my Qt Embedded for Linux installation.
I googled gnome for ubuntu 12.04 and found these instructions. You'll have to see which version of Ubuntu you have and search for that of course. You can see which version you have by typing into a command line:
lsb_release -a
Once I had gnome installed, I restarted my computer and signed in using Gnome.
Then I completely uninstalled and removed all traces of Qt Embedded:
cd yourQtEmbeddedDir
sudo make uninstall
cd ..
rm -r yourQtEmbeddedDir sourceFileTarYouHadDownloaded.tar.gz
I redownloaded the source file tar for Qt Embedded for Linux (from here) and proceeded to install according to these instructions after extracting the source files from the tar:
./configure -embedded -opensource -confirm-license -verbose -qvfb
make
sudo make install
Now, if you tell QtCreator about qmake from this installation, then QtCreator will no longer complain about a bad installation! Ta da!
Note: If you're attempting to the do the Virtual Framebuffer business too, then this is not the end of the road. You need to have Qt for X11 installed as well in order to compile qvfb.
Long story short: You need Gnome if you're trying to install Qt Embedded for Linux with a Virtual Framebuffer on Ubuntu!
I am experiencing the same rJava problem that many other people seem to of had at one point or another. The error occurs when R CMD INSTALL tests whether JNI programs can be compiled.
The output recommends running R CMD javareconf -ed or sudo R CMD javareconf The output of the latter is :
computer: home$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_31
Java home path : /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
JNI linker flags : -framework JavaVM
JNI cpp flags : -I$(JAVA_HOME)/include
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.
And when trying to install rJava afterwards,
computer: home$ R CMD INSTALL ~/Downloads/rJava_0.9-4.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *source* package ‘rJava’ ...
checking for gcc... gcc -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
/* Passes all checks */
configure: checking whether gcc -arch x86_64 -std=gnu99 supports static inline...yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/include'
java libs : '-framework JavaVM'
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rJava’
An alternative attempt where /usr/bin/javac is replaced by /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Homefails just the same.
I am running Mac OS 10.7.3 and
computer: home$ java -version
java version "1.6.0_31"
Java(TM) SE Runtime Environment (build 1.6.0_31-b04-415-11M3646)
Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01-415, mixed mode)
The following is in my .bash_profile
export JAVA_HOME=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Additionally, I have the same problem on Red-Hat. I hope any fix provided will work there too, but if it won't and why it won't is know, please explain.
I've been using this site's incredible knowledge base for a couple of years now, but this is my first post. Mucho thanks in advance.
Some (not all) of the resources I have already browsed through are
https://stat.ethz.ch/pipermail/r-devel/2008-November/051224.html
https://stat.ethz.ch/pipermail/r-help/2008-October/177688.html
R: rJava package install failing
Please note that the apt-get solution in the last link is of no use to me (I think) unless there is an equiv solution for port and/or yum.
I am using Redhat Linux 7.1
I was getting the same problem as above and I performed the following steps
1) Edit /usr/lib64/R/etc/Renviron and add "CPPFLAGS=${CPPFLAGS-'-ldl'}" to the end of the file
2) Then find the java home and set it like below ( set java home till /jre)
$export JAVA_HOME=/usr/lib/jvm/java-1.7.1-ibm-1.7.1.3.10-1jpp.1.el7_1.x86_64/jre
$export PATH=$PATH:$JAVA_HOME/bin
$R CMD javareconf
3) invoke R from commandline
$R
> install.packages("rJava")
> install.packages("RJDBC",dep=TRUE)
> q()
Save workspace image? [y/n/c]: y
I had a recent variation on this same problem with RHEL 6.5. I reviewed this thread and many others. The ptoblem was that the dynamic load modules were not found when testing the complile of the JNI programs. My fix was to insert "CPPFLAGS=${CPPFLAGS-'-ldl'}" into file
/usr/lib64/R/etc/Renviron