Rserve : ld: library not found for -lssl - r

I am getting an error while trying to install Rserve 1.8.6. I can successfully install 1.7.3 from CRAN. This is on Mac OS High Sierra.
ld: library not found for -lssl
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [forward] Error 1
make: *** [all] Error 2
ERROR: compilation failed for package ‘Rserve’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rserve’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rserve’
The downloaded source packages are in
‘/private/var/folders/v7/hyxrfmk94p1_03gdrm27fnxncy3vq1/T/RtmpFHKNMe/downloaded_packages’

This worked for me (MacOS):
In terminal:
brew install openssl
export LIBRARY_PATH=$LIBRARY_PATH:/usr/local/opt/openssl/lib/

I'm running Mac OS 10.15 Catalina, I've spent 2 days trying to fix this same problem, scouring the internet for help. I finally managed it by cobbling together solutions from a few different sources.
The key thing I was missing was that Mac OS ships with its own version of openssl which it thinks is superior to anything else you can find. It is wrong. What you need to do is go and download the latest version of openssl, install that, then export THAT library to your library path variable. Here are the steps I took with openssl 1.1.1:
Get the version number for the latest version of openssl from the source (https://www.openssl.org/source/) and then manually install it directly where it's supposed to go:
cd /usr/local/src
If you're getting "No such file or directory", make it:
cd /usr/local && mkdir src && cd src
Download openssl using curl (shown) or using the link above to the source code (make sure you put the file in the directory you just made in the previous step):
curl --remote-name https://www.openssl.org/source/openssl-1.1.1f.tar.gz
Extract and cd in:
tar -xzvf openssl-1.1.1f.tar.gz
cd openssl-1.1.1f
Compile and install (these are the 64 bit Mac OS instructions. Refer to the openssl documentation for 32 bit and other OS instructions):
./Configure darwin64-x86_64-cc shared enable-ec_nistp_64_gcc_128 no-ssl2 no-ssl3 no-comp --openssldir=/usr/local/ssl/macos-x86_64
make depend
sudo make install
This created a new openssl folder so when you export the library path you have to feed it the right openssl folder:
export LIBRARY_PATH=$LIBRARY_PATH:/usr/local/opt/openssl#1.1/lib/
Hope that helps you if you haven't figured it out yet, and anyone else in the future who is ready to chuck their computer across the room, like I was.

Related

not able to install GCC on Solaris 11.4

I installed Solaris 11.4 x86 in VirtualBox. I need to install the GCC compiler so that I can run c code in Solaris. But each time I try to install the package this error occurs:
Errors were encountered while attempting to retrieve package or file data for the
requested operation. Details follow:
http protocol error: Unknown error code: 500 reason: Internal Server Error
URL: 'http://pkg.oracle.com/solaris/release/solaris/file/1/53eb07cd6fade116a6fdea7397c6839929ec0925'
publisher information:
I have used the following commands:
sudo pkg install developer/gcc/gcc-c-7
also tried -nv option
sudo pkg install -nv gcc
sudo pkg install -nv gcc-7
sudo pkg install -nv developer/gcc-7
see the output of the following command:
kashif#OS:~$ pkg list | grep GCC
output:
system/library/gcc/gcc-c++-runtime 7.3.0-11.4.0.0.1.14.0 i--
system/library/gcc/gcc-c++-runtime-7 7.3.0-11.4.0.0.1.14.0 i--
system/library/gcc/gcc-c-runtime 7.3.0-11.4.0.0.1.14.0 i--
system/library/gcc/gcc-c-runtime-7 7.3.0-11.4.0.0.1.14.0 i--
image below shows gcc package information from repostiry
I am trying to solve this problem for 2 days. I have read documentation from
https://docs.oracle.com/cd/E37838_01/html/E60979/publisher-config.html
I also tried to install developerstudio 12.6 but it didn't work.
overall picture of error and command:
I have googled for errors tried to find information about errors and searched for how to install GCC on Oracle Solaris 11. I couldn't find any solution to this problem.
Try "wget http://pkg.oracle.com/solaris/release/p5i/0/developer%2Fgcc.p5i" or your preferred gcc package and manually install it with pkg install. You can try:
pkg install -v
after downloading.

OSX Installing Rsymphony - linking headers and libs

symphony is correctly installed and tested in terminal. R complains about missing header and libraries when trying to install Rsymphony from source. Any pointers are HIGHLY appreciated. thank you!
symphony installation directory: /Users/timo/Applications/symphony/
R install command:
install.packages("Rsymphony", configure.args="--with-SYMPHONY-include=/Users/timo/Applications/symphony/include/ --with-SYMPHONY-lib=/Users/timo/Applications/symphony/lib",type="source")
results in :
* installing *source* package ‘Rsymphony’
** package ‘Rsymphony’ successfully unpacked and MD5 sums checked
Cannot find SYMPHONY libraries and headers.
See <https://projects.coin-or.org/SYMPHONY>.ERROR: configuration failed for package ‘Rsymphony’* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsymphony’* restoring previous‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsymphony’
I also struggled to get Rsymphony installed, but finally got it working after many hours of messing around. Here's what I did, hopefully it'll save others some time. This works on Mac OS El Capitan (10.11) and R 3.3.0.
First, install the homebrew package manager if you don't already have it:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Next install SYMPHONY with homewbrew. I found this to be the best approach because it puts everything in the right place:
brew tap coin-or-tools/coinor
brew install symphony
Now install pkg-config, a tool for querying installed libraries for when compiling software source code. Not sure if this is strictly necessary, but pkg-config is used in the configuration script for Rsymphony:
brew install pkg-config
At this point Rsymphony should now be able to find the necessary SYMPHONY libraries, however, I still got the following compiler error:
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
Apparently it has something to do with needing a different version of the fortran compiler. This helpful post with instructions for getting the correct compiler saved me. Run the following commands:
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
Now, finally, you should be able to install Rsymphony with:
install.packages("Rsymphony", type = "source")
SOLUTION:
I have found the solution in this link (...I got RSymphony to install, but it involved some hacking ...)
Installing RSymphony using RStudio on macOS
I had also this issue: ..no checking for COIN-OR package CoinUtils... and it was solved by "export PKG_CONFIG=/usr/local/bin/pkg-config; export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig/"

GLPK: No such file or directory error when trying to install R package

I am trying to install sparkTable in R 3.1.0 which depends on Rglpk. I manually installed GPLK on the system and added the libs folder to LD_LIBRARY_PATH before going into R for the install.packages("sparkTable") procedure. I get this error during the installation process. Any ideas?
* installing *source* package ‘Rglpk’ ...
** package ‘Rglpk’ successfully unpacked and MD5 sums checked
** libs
/bin/sh: line 0: cd: GLPK: No such file or directory
make: *** [GLPK.ts] Error 1
ERROR: compilation failed for package ‘Rglpk’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/Rglpk’
ERROR: dependency ‘Rglpk’ is not available for package ‘sparkTable’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/sparkTable’
sudo apt-get install libglpk-dev
did the trick for me.
I had this problem and took a good bit of digging in the package to understand what was happening. If Rgplk can't compile its test program when installing, it does something weird, including this bizarre cd to nowhere. Assuming glpk-devel is installed, the reason it can't compile the test program is that it can't find the gplk header as it is in a non-standard directory.
Just set the environment variable CPATH=/usr/include/glpk
and the test program will compile, allowing the package install to proceed normally.
I had this problem too. The following steps solved this issue for me. My current setup:
OS: Scientifc Linux version 6.5 (on a High Performance Cluster Server)
local user, no root access.
GLPK was not installed
Install GLPK in a local directory:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=/home/<username>/GLPK
make
make install
Install Rglpk (0.6-3):
cd ~
wget http://cran.r-project.org/src/contrib/Rglpk_0.6-3.tar.gz
export LIBRARY_PATH=/home/<username>/GLPK/lib
R CMD INSTALL Rglpk_0.6-3.tar.gz
I landed on this page, because I could not update igraph under Windows 10/11, since igraph also requires glpk as per OP. Specifically:
igraph_glpk_support.h:36:10: fatal error: glpk.h: No such file or
directory #include <glpk.h>
^~~~~~~~ compilation terminated. make: *** [C:/PROGRA~1/R/R-4.1.1/etc/x64/Makeconf:238: feedback_arc_set.o] Error
1 ERROR: compilation failed for package 'igraph'
removing 'C:/Users/xxx/Documents/R/win-library/4.1/igraph'
restoring previous 'C:/Users/xxx/Documents/R/win-library/4.1/igraph' Warning
in install.packages : installation of package ‘igraph’ had non-zero
exit status
I am under Windows 11 (but would be same for Windows 10).
Simple resolution is suggested here:
start Rtools Bash (found in all apps, Rtools 4.0 in the Windows menu)
Run pacman -S mingw-w64-x86_64-glpk and confirm with yes (y)
Run pacman -S mingw-w64-x86_64-libxml2 and confirm with yes (y)
Updating igraph in Rstudio now leads to a clean
DONE (igraph)
(there is no need to install anything, add any path, etc... just the above 4 steps)
In ubuntu 14.04, all above doesn't work. the following however works, without the need of installing libglpk-dev using apt-get.
download the glpk package from gnu and extract it:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.55.tar.gz
tar xvf glpk-4.55.tar.gz
make a GLPK directory in your local path:
mkdir ~/GLPK
configure within glpk:
cd glpk-4.55
./configure --prefix=$HOME/GLPK
cd ..
export LD_LIBRARY_PATH=$HOME/GLPK/lib
export LIBRARY_PATH=$HOME/GLPK/lib
export CPATH=$HOME/GLPK/include
download the Rglpk package from cran and extract it:
wget http://cran.r-project.org/src/contrib/Rglpk_0.6-0.tar.gz
tar xvf Rglpk_0.6_0.tar.gz
move the glpk directory into Rglpk/src and rename it to GLPK:
mv glpk-4.55 Rglpk/src/GLPK
now you can install:
R CMD INSTALL Rglpk
now a bit of explanation of what's going on. The "src/Makevars.in" file in the Rglpk package contains a line of code to enter a non-existing directory 'GLPK' within the src/ folder:
(line 11 of Makevars.in)
GLPK.ts:
#(cd GLPK && make)
touch $#
this is where the problem arises. obviously the code is trying to build glpk within that directory for some unknown reasons. and the solution above is achieved simply by moving the downloaded (and configured) glpk directory there...
If you're on a Debian-based Linux distribution, run this to install GLTK:
sudo apt install libglpk-dev
If you're on MacOS, run this to install GLTK:
brew install gltk
Finally, install the R library:
install.packages("Rglpk")
On Centos, have sudo rights. None of the above worked, but had to install GLPK in /usr/local as suggested in this SO answer. Been trying to install it for about 3 hours fml
You must install glpk dependency first.
On macOS (via homebrew):
brew install glpk
or in RStudio (via homebrew):
system("brew install glpk")
It worked for me when I combined the answers from Simón Ramírez Amaya and shadowleaves:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=$HOME/GLPK
make
make install
cd ..
export LD_LIBRARY_PATH=$HOME/GLPK/lib
export LIBRARY_PATH=$HOME/GLPK/lib
export CPATH=$HOME/GLPK/include
wget https://cran.r-project.org/src/contrib/Rglpk_0.6-4.tar.gz
R CMD INSTALL Rglpk_0.6-4.tar.gz
To load the library
dyn.load(file.path(Sys.getenv("HOME"), "GLPK", "lib", "libglpk.so"))
library(Rglpk)
The answer of Zhiying Cui is right, however, if your script has some special codes, such as foreach for parallel computing, it may raise an error.
A better way is as fellow
If your os is Centos, try
yum install glpk-devel
then just go to R or Rstudio server and
install.packages("Rglpk")

native client tutorial can't find libstdc++

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).

Undefined reference to QIconvCodec during Qt embedded make?

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!

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