compiling programs in scientific linux (pcre) - unix

I'm currently trying to install gtk3 on scientific linux (It is not available on official repositories)
I'm well used to yum, apt, pacman etc but i'm a little lost here when it's about compiling ...
to install gtk3, i need glib, to install glib, i need pcre 8.32.
I thus downloaded the tarball from their site.
Once 'untarred', i followed what is written on that link :
http://www.linuxfromscratch.org/blfs/view/svn/general/pcre.html
but once i've made './configure' with its options, 'make', and then 'make install' glib doesn't configure any better... it says my version is still the old version
configure: error: Package requirements (libpcre >= 8.13) were not met:
Requested 'libpcre >= 8.13' but version of libpcre is 7.8
The files seems to be well compiled but not 'moved correctly to the right place' ...
Did i miss something ?
By the way moving to another distro is not an option :P

Related

How to Install qt4 on macOS with homebrew?

I need to install the qt4 C++ framework for one of my classes. I tried using the regular installer from the download archives page for both qt4.7 and qt4.8, however I get the warning:
"Installing this package may damage your system, and the installation may fail."
So I looked into installing it via homebrew and initially tried:
brew tap cartr/qt4
brew tap-pin cartr/qt4
brew install qt#4
However, that gives me this error:
Error: Calling brew tap-pin user/tap is disabled! Use fully-scoped user/tap/formula naming instead.
I looked online for a solution and was able to install it by omitting the brew tap-pin cartr/qt4 command:
brew tap cartr/qt4
brew install qt#4
I then tried to create a sample qt program in the CLion IDE and checked the version I was using, and it said I was using qt5 (from the python anaconda distribution). So my question is, can I install both qt4 and qt5 on my system simultaneously? How do I select which version to use?
You can install both simultaneously. You can select which to use.
When you install qt (meaning qt5) using homebrew, it produces a "Caveats" message that answers your question.
It says will need to set certain environment variables yourself.
It says that, in only those shell sessions where you set those environment variables, qt (meaning qt5) will be available.
It says, if you want qt always available, then you can simply put those settings in your dot files.
If you install qt#4 and set those same variables to point to qt#4, then qt#4 will be available instead.
You can view the same "Caveats" message again using brew info qt. Here is the whole message:
qt is keg-only, which means it was not symlinked into /usr/local,
because Qt 5 has CMake issues when linked.
If you need to have qt first in your PATH run:
echo 'export PATH="/usr/local/opt/qt/bin:$PATH"' >> ~/.zshrc
For compilers to find qt you may need to set:
export LDFLAGS="-L/usr/local/opt/qt/lib"
export CPPFLAGS="-I/usr/local/opt/qt/include"
For pkg-config to find qt you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/qt/lib/pkgconfig"
The same commands with qt#4 made qt#4 available for me:
export PATH="/usr/local/opt/qt#4/bin:$PATH"
export LDFLAGS="-L/usr/local/opt/qt#4/lib"
export CPPFLAGS="-I/usr/local/opt/qt#4/include"
export PKG_CONFIG_PATH="/usr/local/opt/qt#4/lib/pkgconfig"
By the way, I installed qt#4 using the user/tap/formula syntax: brew install cartr/qt4/qt#4

installing R 3.3.2 in HOME directory in centos

I am trying to install R 3.3.2 on a server running centos 6. I have to install it in my Home directory on the server because i don't have the permissions anywhere else. I downloaded it using wget and then tar. But when I reach the point of "./configure" in order to run "make" afterwards it stops with an error.
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are required
I installed zlib 1.2.8 and added its path to my bash_profile then tried to run the command ./configure for the R again but i got the same error. It seems that it still sees that I am using an old version of zlib (1.2.3) (The one that is already installed on the server). Have anyone had a similar issue or have any advices regarding this ? Thanks in advance
and added its path to my bash_profile
I am curious if you prepended or appended the path. In the latter case, configure will detect the old zlib.
In order to prepend, do like
export LD_LIBRARY_PATH=/path/to/zlib/inst/dir/lib:${LD_LIBRARY_PATH}

pip says that module has already been installed while python

Now a bit of background of my current setup:
I have Python3.3 running on Centos 6. I'm currently working on a web application using Flask that runs on Apache 2.2.15 with mode WSGI 4.5.3 and virtualenv 15.0.2.
pip --version pip 8.1.2 from /usr/local/bin/lib/python3.3/site-packages (python 3.3)
I have installed pysvn with pip and when I run pip show pysvn says
Location: /usr/local/bin/lib/python3.3/site-packages
755 permissions recursively set to /usr/local/bin/lib/python3.3/site-packages. And I passed --system-site-packages argument to virtualenv to use the global site packages.
Even when I try to import the package from python interpreter it does not work. So it is not specific to my virtualenv setup but rather a global problem.
I must mention that other packages installed with pip work perfectly fine (i.e. flask).
I've exhausted all other avenues before coming forward to you guys. Any suggestion would be highly appreciated as I ran out of ideas.
L.E.
I did manage to install it in the end. I'm not completly sure yet why and how but I presume is was compatibility issue.
First of all I have uninstalled svn 1.6+ and installed version 1.8.16 instead which seems to be tested against the latest two versions.
Second, I have uninstalled the troublesome pysvn instance and installed pysvn-1.8.0 workbench "sudo /var/www/FlaskApp/FlaskApp/flask/bin/pip install pysvn-1.8.0.tar.gz". In this case I have installed it my local environment. The 1.9.0 version of pysvn did not work.
L.L.E.
False positive, still doesn't work. I'm going to interact with svn via command line from my script.
L.L.L.E.
After installing svn 1.8.16 and svn-devel along with the rest of dependencies described in the readme file I have managed to successfully install it from the source fallowing the instructions.
Thanks for your help Barry.
pysvn is not available from PyPI because PyPI has no way to allow me to upload pysvn for each supported SVN version. Let alone deal with the issues of installing on a Linux distro given the choices for pysvn dependencies.
(APR, SVN, OpenSSL etc).
Fedora packages pysvn for the Fedora release.
I'm assuming that means it is on RHEL and therefore packaged by CentOS.
(But I do not have RHEL or CentOS to check this on)
If you find that a package is not available for your CentOs is not hard
to build pysvn on a linux distro. Get the source kit and follow the readme.html should get you going.
Barry (pysvn maintainer)

Install and run frama-C in Windows 7

I have tried to run the Frama-C on windows 7, but it didn't work.
I have read all the tips and comments you wrote here, but still not working.
Can someone explain the installation process is a clear and simple way, and I will grateful?
The easiest install for Windows 7 is to use the Windows binary installer for the Boron release (http://frama-c.com/download/frama-c-Boron-20100401.exe). If you do install this version, you will still need to install the gcc-preprocessor in order for frama-c to build your source code.
Newer releases (i.e., Sodium) require you to build from the source code distribution, which means you will need to install several prerequisites as listed in the install instructions:
GNU make version >= 3.81
Objective Caml >= 3.12.1 (except 4.02.0);
a C compiler with standard C and POSIX headers and libraries
The Frama-C GUI also requires:
Gtk (>= 2.4)
GtkSourceView 2.x
GnomeCanvas 2.x
LablGtk >= 2.14.0 (and >= 2.18.2 if you use OCaml >= 4.02.1)
If you need to build from source, please comment and I will give you the steps to complete that.
fdopen's OCaml for Windows allows installing OPAM with a special repository.
Once you have it, installing Frama-C requires only a few steps:
# install depext, for external dependencies
opam install depext
# help Cygwin installing dependencies
opam install depext-cygwinports
# install Frama-C dependencies
opam depext frama-c
# install Frama-C itself
opam install frama-c
Frama-C on Windows installation instructions are periodically updated on Frama-C's wiki.

qpdf.exe for compactPDF?

I am trying to check a package that I have built (with vignette) using R CMD check --as-cran [my package] in my windows command prompt. All goes well until I get the message,
WARNING 'qpdf' is needed for checks on size reduction of PDFs
I have downloaded qpdf, put the unzipped folder in my program files directory, and added the bin folder to the PATH.
Not quite sure what else I need to do? I have the feeling I have not installed qpdf correctly or I need to build this program itself? I have read through the readme files and manual for qpdf which appear to be more aimed at unix users (which I have no experience with... I am your standard/regular windows user with little to no programming experience outside of statistical languages). I have had a go at trying to build qpdf using cgywin, but ended up failing to install zlib and prec. Any tips?
I would try
Sys.which(Sys.getenv("R_QPDF", "qpdf"))
Sys.getenv("PATH")
to establish that R is really not finding the qpdf executable, and see where it is looking. You probably shouldn't need to rebuild everything, just figure out why R is not finding the qpdf executable ... does running qpdf from a terminal window work ... ? How are you starting R, and did it have a chance to get the new PATH definition (i.e. do you need to open a new terminal window, or ?? reboot ??)
The incantation above was extracted from tools::compactPDF, from the default value of the qpdf argument, on a Linux machine. You should check for yourself, in case (e.g.) the Windows version is looking for qpdf.exe rather than qpdf ...
There are a couple of other things to consider on a Windows machine:
If you are running the 32-bit version of R, it is important that you download the 32-bit version of qpdf, which is the version linked from the SourceForge homepage. If you are running a 64-bit installation of R, you will need to do a bit of digging to locate the 64-bit version of qpdf, which is buried a little more deeply (version 7.0 is listed here).
Once you have extracted the zipped qpdf directory to your hard disk, perhaps under C:\Program Files\, added C:\Program Files\qpdf-version_number\bin to your system PATH under the environment variables, and re-launched R, Windows needs to establish that pqdf is safe to run.
Navigate to C:\Program Files\qpdf-version_numer\bin and execute qpdf.exe (by double-clicking). Windows 10 throws up a security warning, as it's an unrecognized executable file. You'll need to use the more options link to find the button to run the program. This done, Windows will recognize the file as safe to run and allow other software, including R, to use it.
Recent developments: If you install Rtools 3.5 qpdf is included and that warning is gone. Rtools is a toolset for building packages on Windows and is recently reworked by Jeroen Ooms.
More information : https://cran.r-project.org/bin/windows/Rtools/
Note that the changelog is incomplete, as Rtools 3.5 isn't frozen yet at the time of writing (2019-03-01). Even though it's not visible on the page yet, qpdf.exe is included in the bin directory after installation.
After installing the latest version of RTools, the warning still popped up.
However, I noticed that the Windows "where" command gave two paths to qpdf (different versions). After removing the R_QPDF environment variable and removing the new install of qpdf from the Windows path, so that only qpdf in RTools was found, the warning disappeared.
I got the same warning on Ubuntu so here's a Ubuntu solution for completeness:
First update packages
sudo apt update
Then install qpdf with
sudo apt install qpdf
Tested on Ubuntu 20.04.

Resources