"xcode-select --install" versus retrieving the dmg from Apple's developer website I would to ask a question closely related to already existing posts (How to install command line tools without error that is not currently available on Software Update server? and https://stackoverflow.com/questions/19691701/failed-to-install-command-line-tools-on-osx-mavericks) but with the help of which I still could not fully solve my problem. 

I have a MacBook Pro running Mac OSX 10.9. When I run xcode-select --install  from the terminal, the command fails with an error message Can't install software because it is not currently available from the Software Update Server (see second linked post for screenshot).

It was suggested by many to simply download the command line tools package from the developer website, which I have done (already had an account). My question, is the second procedure strictly equivalent to running xcode-select --install? I have suspicions that the paths to the different libraries and headers are not defined in the same way when downloading and executing the dmg. 

I am running particle physics software called root and compiling with the available C++ interpreter fails with "Undefined symbols for architecture x86_64" error, probably due to the use of standard libc++ instead of libstdc++. Strangely enough this problem does not appear on another computer (running same OSX 10.9) where I was able to run the xcode-select --install command.

Is there any way to solve this error message when running xcode-select --install? People have suggested this could be due to the fact that command line tools are already installed but I have both tried deleting command line tools by hand (sudo rm -rf /Library/Developer/CommandLineTools) and even a clean install of Mavericks but no luck.
Are you sure they are installing the same version?

At the command line on both machines run cc -v - the latest version seems to be Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn).