Installation of doxygen and error in make command - makefile

I am trying to install doxygen in my CentOs 6.3 machine and I am getting this error. Any ideas??
[root#dell1 doxygen-1.8.3.1]# make install
/usr/bin/install -d /usr/local/bin
/usr/bin/install -d /usr/local/doc/doxygen
/usr/bin/install -m 755 bin/doxygen /usr/local/bin
/usr/bin/install -m 755 bin/doxytag /usr/local/bin
/usr/bin/install: cannot stat `bin/doxytag': No such file or directory
make: *** [install] Error 1

Bash isn't wrong in complaining:
/usr/bin/install: cannot stat `bin/doxytag': No such file or directory
It happens to be that the compiled file doxytag was not included in the downloaded tar file. So when you try to make, it couldn't find that file. To make it successfully, you have two options:
Compile the doxytag.py file from here and paste it to doxygen's bin directory
You can compile the python file doxytag.py from the above link using:
python -m compileall path_to_the_file/doxytag.py
It should generate a python compiled executable with .pyc extension. Now move this file to your doxygen-version folder. For example,
mv doxytag.pyc your_path/doxygen-1.8.5/bin/doxytag
Or alternatively download the doxytag from here
Now when you try to make, it will complete without any errors.
Comment out the line that requires doxytag file from the Makefile
You may read about the doxytag utility from https://www.star.bnl.gov/public/comp/sofi/doxygen/doxytag_usage.html.
If you do not really require this utility in your documentation, simply skip it by commenting out or deleting the line in the Makefile present in the doxygen-1.8.5(as per your version) directory by:
#$(INSTTOOL) -m 755 bin/doxytag $(INSTALL)/bin
And then run the make command.

The doxygen make is strange: "make install" will not invoke "make", so you need to do a
make
make install
to first generate the binaries and then install them.

A cannot stat error literally means the file(s) or directory does not exist - or you do not have the correct permissions. If you know where the directory is located - start looking there for permissions and file existence.

Try as a superuser.
sudo make install

First, you'll need to install some dependencies.
sudo apt install cmake
sudo apt install flex
sudo apt install bison
After that, execute the commands below; it'll probably work fine.
git clone https://github.com/doxygen/doxygen.git
cd doxygen
mkdir build
cd build
cmake -G "Unix Makefiles" ..
make
sudo make install

Related

Can't install apertium language packages from source - make command shows errors

I am trying to install apertium-eng-ita package from source (available at https://github.com/apertium/apertium-eng-ita). The system is debian 11 (i tried also on fresh ubuntu, get the same error). So i downloaded all the files into my /root directory (/root/eng-ita contents all the files from provided link) and run:
./autogen.sh
This generated all the necessary files inside the "eng-ita" folder, including "Makefile". But then i run:
make
and see errors like:
apertium-validate-dictionary apertium-eng-ita.eng-ita.dix /bin/bash:
apertium-validate-dictionary: command not found make: ***
[Makefile:769: eng-ita.autobil.bin] Error 127
I began googling (for example, here is some info - https://wiki.apertium.org/wiki/Installation_troubleshooting) this 127 error and found some information about PATH, but where i can put this PATH to make it work?
If you're installing from source, you should first add the apt source and install apertium-all-dev which will give you make etc. Cf. https://wiki.apertium.org/wiki/Prerequisites_for_Debian you should
curl -sS https://apertium.projectjj.com/apt/install-nightly.sh | sudo bash
sudo apt-get -f install locales build-essential automake subversion git pkg-config \
gawk libtool apertium-all-dev
(But you don't need to install from source if you just want to use the pair and not develop for it. There are nightly debian packages of the latest git commit; after running the first command you can get that package with sudo apt install apertium-eng-ita)

Protobuf cannot find shared libraries

I have installed protobuf by using following commands:
./configure
make
make check
make install
However when I run protoc I get following error:
protoc: error while loading shared libraries: libprotoc.so.8: cannot open shared object file: No such file or directory
sudo ldconfig
or
export LD_LIBRARY_PATH=/usr/local/lib
should solve the problem.
You can also use
$ sudo ldconfig # refresh shared library cache.
as stated at the installation page
This issue can be resolved by following these steps:
vim /etc/ld.so.conf
/usr/local/lib(add it in .conf)
This issue can be resolved by following these steps:
sudo make uninstall
sudo make distclean
sudo make clean
./configure --prefix=/usr
This cleans the current installation and installs protobuf at /usr
Run ldconfig to update ld.so.cache after making sure that /usr/local/lib is listed in /etc/ld.so.conf. i.e.
Edit /etc/ld.so.conf and append /usr/local/lib to it and run ldconfig

Installing glib in non-standard prefix fails

I'm trying to install glib in a non-standard prefix but I get the following when running make install:
/bin/sh ../libtool --mode=install /usr/bin/install -c libgthread-2.0.la '/root/build/lib'
libtool: install: error: cannot install `libgthread-2.0.la' to a directory not ending in /usr/local/lib
Any reason why I have to install gthread only in a prefix ending with /usr/local/lib?
I also just stumbled over that problem when compiling MonetDB on my Linux machine. Here is the solution/workaround that worked for me: Always make clean after ./configure.
In your example you should be able to do:
./configure --prefix=/root/build && make clean && make && make install
I found the solution in a discussion on an apache httpd bug where Joe Orton shares his knowledge:
A "make clean" is usually necessary after re-running "configure".
Using:
make clean
make distclean
Works for me.
The install path of a library can usually be customized rather than the default one under somewhere /usr/local/.
For some libraries, you should specify it with ./configure like this:
./configure --prefix=/the/new/install/path
make
make install
Others allow you to specify it when make install:
./configure
make
make install prefix=/the/new/install/path
You can try both. At least one should resolve your issue.

How to rectify issues occurring while installing Cufflinks and Boost?

I'm having a problem installing Cufflinks. Before installing Cufflinks, I installed Boost first with:
bjam --prefix=/Users/jimmy/Downloads/boost_1_46_1/ toolset=gcc link=static install
It seems to be ok.
However, when installing Cufflinks, it seems there is a problem in the installation of Boost. See error below:
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.
dhcp128036164110:cufflinks-1.0.3 jimmy$ ./configure --prefix=/Users/jimmy/Downloads/ --with-boost=/Users/jimmy/Downloads/boost_1_46_1/
If I missed something, could you tell me what is wrong now? Thanks.
PS: I am using Mac OS X (not Windows)
Here is a complete procedure I used for installing Cufflinks from source on a Linux Redhat 64-bit system without root privileges.
Install Boost
1. Create a directory to install into
mkdir ~/bin/boost_1_55_0
2. Download Boost
wget http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz
3. Unpack Boost
tar xzvf boost_1_55_0.tar.gz
4. Change into boost directory
cd boost_1_55_0
5. Run bootstrap.sh script
./bootstrap.sh
6. Run b2 script
./b2
7. Run b2 script again to install
./b2 install –prefix=/lustre/home/jernest1/bin/boost_1_55_0
8. Add installation directory to several environment variables in ~/.bashrc
Add /lustre/home/jernest1/bin/boost_1_55_0/lib to LD_LIBRARY_PATH
Add /lustre/home/jernest1/boost_1_55_0 to a new variable BOOST_ROOT
Add /lustre/home/jernest1/boost_1_55_0 to a new variable CPLUS_INCLUDE_PATH
9. Source ~/.bashrc
source .bashrc
Install SAM tools
1. Download sam tools
wget http://sourceforge.net/projects/samtools/files/samtools/0.1.17/samtools-0.1.17.tar.bz2
2. Unpack
tar jxvf samtools-0.1.17.tar.bz2
3. Move into the samtools directory
cd samtools-0.1.17
4. Run make
make
5. Make new directories to put sam library files if they don’t already exist
mkdir –p ~/bin/lib
mkdir –p ~/bin/include/bam
6. Copy the libbam.a file to ~/bin/lib/
cp libbam.a ~/bin/lib/
7. Copy header files into ~/bin/include/bam/
cp *.h ~/bin/include/bam/
8. Copy the samtools executable program to a directory in your PATH
cp samtools ~/bin/
9. Add the bam directory to the new variable BAM_ROOT in ~/.bashrc
Install Eigen libraries
1. Download Eigen libraries
wget http://bitbucket.org/eigen/eigen/get/3.2.3.tar.gz
2. Unpack
tar xzvf 3.2.3.tar.gz
3. Move into Eigen directory
cd eigen-eigen-36fd1ba04c12
4. Copy the Eigen subdirectory into ~/bin/include/
cp -r eigen-eigen-36fd1ba04c12/Eigen/ ~/bin/include/
Install Cufflinks
Option 1: Install an official release
1. Make a directory to hold the installation.
mkdir cufflinks_2.2.1
2. Move into that directory
cd cufflinks_2.2.1
3. Download cufflinks
wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz
4. Unpack
tar xzvf cufflinks-2.2.1.tar.gz
cd cufflinks-2.2.1
5. Run configure script
./configure --prefix=/lustre/home/jernest1/cufflinks_2.2.1 --with-eigen=/lustre/home/jernest1/eigen-eigen-36fd1ba04c12/Eigen --with-bam=/lustre/home/jernest1/bin --with-boost=/lustre/home/jernest1/bin/boost_1_55_0
6. Run make
make
7. Run make install
make install
Optionally, copy ~/cufflinks_2.2.1/bin/cufflinks into ~/bin/
Option 2: install from Github project
1. Make directory to install into
mkdir cufflinks_2014-12-11
2. Move into that directory
cd cufflinks_2014-12-11
2. Download Github project
Click on the "HTTPS clone URL" button to save the URL location to your clipboard
Download
git clone https://github.com/cole-trapnell-lab/cufflinks.git
4. Run autogen.sh to convert configure.ac into configure
./autogen.sh
5. Run configure script
./configure --prefix=/lustre/home/jernest1/cufflinks_2014-12-11 --with-eigen=/lustre/home/jernest1/eigen-eigen-36fd1ba04c12/Eigen --with-bam=/lustre/home/jernest1/bin --with-boost=/lustre/home/jernest1/bin/boost_1_55_0
6. Run make
make
7. Run make install
make install
Optionally, copy ~/cufflinks_2014-12-11/bin/cufflinks into ~/bin/

problems at installation of sphinx on mac osx - can't even do the ./configure command

I tried to install sphinx on my Mac (OSX 10.6.7) but at the first installation step, I run into a problem.
According to the installation doku, http://sphinxsearch.com/docs/current.html#installation, one should do the following steps
$ ./configure
$ make
$ install
When I enter ./configure in my terminal, I get the following error message:
$ ./configure
> -bash: ./configure: No such file or directory
So I looked in the folder 'sphinx-2.0.1-beta-osx10.6-i386' and saw that there's no such file such as configure. Also
$ ls -a
> . api doc sphinx-min.conf.in
.. bin example.sql sphinx.conf.in
COPYING contrib log
INSTALL data sphinx-min.conf
When I tried other files such as sphinx-min.conf, I get
$ ./sphinx-min.conf
$ -bash: ./sphinx-min.conf: Permission denied
Also the sudo ./sphinx-min.conf doesn't work
$ sudo ./sphinx-min.conf
$ sudo: ./sphinx-min.conf: command not found
Any ideas?
It seems possible that you have downloaded a binary version, rather than the source code. You should check for binaries in the subdirectory bin.
You should also read the file INSTALL, which probably has installation instructions that go with the distribution you have downloaded.
You should download Source tarball (tar.gz) from http://sphinxsearch.com/downloads/release/ even it has the deceptive linux-penguin icon. After decompression the tarball you can follow the installation steps as http://pat.github.com/ts/en/installing_sphinx.html says.

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