copycat: Change magic-static to magic

[sjackman]

Fix the error:

ld: library not found for -lmagic-static

The file libmagic-static.* does not exist on Ubuntu.
See https://packages.ubuntu.com/search?searchon=contents&keywords=libmagic-static&mode=filename&suite=xenial&arch=amd64

There is however a file name libmagic.so.
See https://packages.ubuntu.com/search?mode=filename&suite=xenial&section=all&arch=amd64&keywords=libmagic.so&searchon=contents

See the failed build log at
https://gist.githubusercontent.com/sjackman/1d82c11853fd4c16bbfa7d0e3f553e2b/raw/543e2b51e6db0eeef42208198a860664892d2d02/08.make
and https://gist.github.com/sjackman/1d82c11853fd4c16bbfa7d0e3f553e2b#file-08-make-cc

[kwrodarmer]

copycat is an NCBI internal tool that is statically linked - we cannot have a dynamic link here. You're welcome to use it if you can figure out something useful, but it is not for external use.

[sjackman]

I have no particular need for copycat. I simply want to run make without it failing. Any suggestions?

[kwrodarmer]

If you are unable to build, then let's file a bug against configuration that it doesn't pick up on the fact that you don't have a static libmagic.

I'm glad you got the build to work, and we're close to a new release - so we can probably make this adjustment quickly.

By the way, we've been planning a big overhaul of the whole make system for a while...

[sjackman]

Why is this option -smagic-static rather than the usual -lmagic-static? I couldn't find a relevant option for -s in the man page for either gcc or ld.

[sjackman]

Ubuntu does install a static library named libmagic.a.
See https://packages.ubuntu.com/search?mode=filename&suite=xenial&section=all&arch=amd64&keywords=libmagic.a&searchon=contents
I don't know of any distribution of Linux that installs a file named libmagic-static.a.

[sjackman]

By the way, we've been planning a big overhaul of the whole make system for a while...

I prefer the autotools myself, autoconf and automake.

[sjackman]

If you are unable to build, then let's file a bug against configuration that it doesn't pick up on the fact that you don't have a static libmagic.

Looks like this line should be -lmagic-static:

-            $library = '-lmagic';
+            $library = '-lmagic-static';

sra-tools/setup/konfigure.perl

Line 1516 in 0597af0

$library = '-lmagic';

[kwrodarmer]

So many comments! Let's see:

1. the option -smagic is interpreted by a linker driver that knows it must perform a static link for this library. We produce our own internal builds of several libraries, and used to build libmagic before this began to break across several hosts. Our own build produces a libmagic-static.a symlink to libmagic.a and it's used as a kludge to prevent the linker from preferring a shared library.

2. Yes, nobody does the *-static.a link trick, and we don't try to depend upon it. I don't know why we're trying to build copycat for you (something I have to look into), but the correct behavior for the build in your case is to not try to build it.

3. Many people prefer autoconf tools. We don't, for many (good) reasons. First, we don't need it; our build was originally perfectly able to do everything it needed with just make. So many people complained that it didn't have a configure step that we added it. Second, autoconf tools are great for producing builds for a particular host, or a golden host for distribution; we build tools that have a much wider distribution than that, and the idea of configuring for a host is absurd. So autoconf is not on the table.

4. I think probably the line should read -smagic.

[klymenko]

How can I reproduce the problem with library not found for -lmagic-static?

I can build copycat on Ubuntu after I installed libmagic-dev.