According to an error message of the compiler this option is available only for 10.5 and higher. The linker command has an option -Wl,-rpath,/sw/lib, which is incompatible with Perl's MACOSX_DEPLOYMENT_TARGET=10.3. This Perl module needs htslib from SAMTools, see Compiling C programs for Ensembl API below for more information. This can be found by looking at the output of perl -V Perl 5.28 by default has this set to 10.3, it probably also works with the variable set to this value. Notice the MACOSX_DEPLOYMENT_TARGET=10.4, which tells OSX to build binaries compatible with 10.4 and higher. LD="env MACOSX_DEPLOYMENT_TARGET=10.4 gcc-fsf-5 -L/sw/lib"' configure-args='CC="env MACOSX_DEPLOYMENT_TARGET=10.4 gcc-fsf-5" This and switching to GCC5 allows compilation, forcing installation as one or two unit tests fail: cpanm install -force IO::Socket::SSL \ cpanm has an experimental option for passing building arguments, –configure-args, as otherwise the library located in /sw is not found. These are listed here.Īs of writing this (), Fink's openssl library did not allow flawless compilation of Net::SSLeay, which is one of IO::Socket::SSL's dependencies. For example, Class::InsideOut is installed with cpanm as follows:įew packages cannot be installed via cpanm, either they are not available or cause problems during compilation. We have tested Dintor on Perl 5.10 (long time ago), 5.14 (as of 2019) and 5.28 (as of 2019, too). Most of the Perl programs can be installed with cpanm from perlbrew. Things get a lot easier, if there are some package managers around. If you do not yourself have admin privileges, consider asking your admin staff to create a linuxbrew role account for you with home directory set to /home/linuxbrew.įollow the Next steps instructions to add Homebrew to your PATH and to your bash shell profile script, either ~/.profile on Debian/Ubuntu or ~/.bash_profile on CentOS/Fedora/Red Hat.Compiling Dintor on Mac OS X is a bit complicated and deserves some more information presented in this document. The prefix /home/linuxbrew/.linuxbrew was chosen so that users without admin access can ask an admin to create a linuxbrew role account and still benefit from precompiled binaries. If you decide to use another prefix: don’t open any issues, even if you think they are unrelated to your prefix choice. The main reason Homebrew just works is because we use bottles (binary packages) and most of these require using the default prefix. Building from source is slow, energy-inefficient, buggy and unsupported. Many things will need to be built from source outside the default prefix. However, you shouldn’t install outside the default, supported, best prefix. Technically, you can install Homebrew wherever you want. Using /home/linuxbrew/.linuxbrew allows the use of most binary packages (bottles) which will not work when installing in e.g. Homebrew does not use sudo after installation. The installation script installs Homebrew to /home/linuxbrew/.linuxbrew using sudo. Instructions for the best, supported install of Homebrew on Linux are on the homepage.
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