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Recently, after the installation of Coreutils, we added a step to manually
run PatchELF over all the contents of the `$(ibdir)'. However, after a
fresh test, this method failed: because while PatchELF was updating `mv',
another program that was using `mv' couldn't do so and crashed.
To fix this problem, Coreutils is now installed in a dummy directory also
and the exact files that need `rpath' are identified and PatchELF is run on
them (to be clean). Also, higher-level `basic.mk' software (higher-level
than Bash), were re-organized so they depend on Coreutils. With this, we
are no sure that when Coreutils is being built, it is the only program that
is being built and PatchELF won't interfere with any other program.
Also, OpenSSL and CMake were set to be bulit in parallel to speed up their
build.
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Especially because of the new convention regarding backslashes, there were
many conflicts that are now fixed. But none were substantial.
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When we need to quote the new-line character we end the line with a
backslash (`\'). Until now, our convention has been to put all such
backslashes under each other to help in visual inspection.
But this causes a lot of confusion in version control: if only one line's
length is larger, the whole block will be marked as changed and thus makes
it hard to visually see the actual change. It also makes debuging the code
(adding some temporary lines) hard.
With this commit, I went through all the files and tried to fix all such
cases so only a single white space character is between the last command
character and the backslash. Where there was an empty line (ending with a
backslash, to help in visually separating the code into blocks), I put the
backslash right under the previous line's.
This completes task #15259.
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Until now, to test if GCC can use `sys/cdefs.h', we were building
a small test program using it. But after testing on an Ubuntu 14.04,
we noticed that the GCC test during the configure script passes, but
GCC still can't be built. After some investigation we noticed its
available in other directories, but during the build of GCC, those
directories aren't used, and it only assumes it to be under
`/usr/include'. So with this commit, we are only checking this
particular location for this header, not a test run of GCC.
After fixing this, we noticed that GCC's build crashed again because
it couldn't link with `libc.a' (or `libc.so'). So we also added a
for this library and added a new warning to inform the user what they
might be able to do.
Finally, we noticed that in one of the last steps of building GCC,
we weren't using `&&', but `;', so the GCC name file would be
built, even when the GCC build failed.
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Even though the Coreutils configure script says that it adds `rpath' to its
executables, its executables don't have it. As a result, it goes to use the
host operating system libraries, causing failures when they don't match
with the template.
Unfortunately after some tests with the configure script, I couldn't find
any way to include `rpath'! Even though `-rpath-link' is present in all
linking commands during Coreutils' build, the installed files still don't
have it!
So I was forced to use PatchELF. However, one problem is that Coreutils
installs many programs, not just one like Bash or AWK.
As a brute-force solution, with this commit, we are running PatchELF on all
the installed programs. It won't hurt those that already have it, but it
will fix all those that don't.
With this commit, I am also making the following non-related small changes:
- In `build-rules.mk', the `&&' characters were placed at the start of the
line for better readability.
- Bash, Readline and NCURSES are now built in parallel on systems that
support it (during `basic.mk').
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Until this commit, `m4' was not a prerequisite of `gmp'. However, during
a test in Ubuntu 14.04 using one single core in the configure step, it
crashed complaining about not having `m4' installed.
With this commit, we set `m4' as a prerequisite of `gmp'.
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With this commit, the copyright information of some files have been
modify in order to include the work of Raul Infante-Sainz.
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Until this commit, in Mac OS we were installing `binutils' as symbolic
links of various programs (`as', `ar', `ld', `nm',` ps' and `ranlib').
However, there was a missing semicolon at the end of each line. As a
consecuence, the installation of `binutils' on Mac OS systems failed.
With this commit, we fix this problem by typing a semicolon at the end
of each makelink line.
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Until now we were using the official tarball of GNU Bash. However, Bash is
distributed using patches, not a public version controlled history. So to
implement newer features of Bash, its necessary to apply those patches and
make the tarball ourselves.
With this commit, we have done just that: we used the 7 patches that have
been released since version 5.0.0 and made a tarball to use for this
template. The instructions on how to make the patched tarball are also
given above the Bash build rule.
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Until now, `metastore' did not depend on the necessaries programs that
we use to install it (`awk', `coreutils' and `sed'). They are not
official dependencies of `metastore', but we need them to install it.
With this commit, we put these programs as prerequisites of `metastore'
in order to be able to install it without any problem.
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Until now, to specify which high-level software you want the project to
contain, it was necessary to go into the `high-level.mk' Makefile that is
complicated and can create bugs.
With this commit, a new `reproduce/software/config/installation/TARGETS.mk'
file has been created that is easily/cleanly in charge of documenting the
final high-level software that must be built for the project.
Also, until now, FFTW was set as a dependency of Numpy while we couldn't
actually get Numpy to use it! It was just there for future reference and to
justify its build rule. But now that many software won't be built and there
is no problem with having rules even though a project might not use them,
it has been removed.
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Git and Metastore are very basic and fundamental tools for the template, so
to keep things clean (let the `high-level.mk' software only represent
optional software in the template), these two software (and their
dependencies: `cURL' and `Libbsd') will now be built in `basic.mk'.
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Until this commit, we didn't install Binutils. However, we need `strip'
for installing Netpbm, and `strip' is part of the Binutil software.
With this commit, we include Binutils as a dependency of GCC for
GNU/Linux systems. For Mac OS systems we create a symbolic link to
`strip' just after the generation of the symbolic link to `gcc'.
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Due to the copy/paste of rules from other files, in some rules there
were some spaces insteand of tab. There were also a lack of semicolon in
the building of CC, and bad extensions in various tarballs.
With this commit, all of these typos have been fixed.
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Until now, we did not have CC. This is an obsolete way of calling C
Compiler, nowadays it is GCC. However, there could be some software
that is still using this convention (for example, `netpbm').
With this commit, we make the symbolic link `cc' pointing to the
installed `gcc'.
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Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.
Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.
Also, some of the software versions were also updated after some checks
with their webpages.
This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).
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