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Until this commit, we had some of the python packages intalled
but they did not work properly because of the `PYTHONPATH' variables.
That is, the pipeline's `python' was the `python' of the system
instead of the pipeline's `python'.
With this commit this issue has been fixed by setting the correct
`PYTHONPATH'. In this commit we also modify the installation of
`bzip2' because `CMake' was complaining about some libraries built
statically.
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Until now, the pipeline was not installing its own `gcc' but using the
system one by making a symbolic link.
With this commit, GNU GCC has been added into the pipeline. Right now
the installation does not work on Mac OS system beause of some conflicts
with `clang', but in principle it should work on GNU Linux distributions.
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Until now, the check to see if the patchelf program should be used or not
(for GNU/Linux vs. Mac installations) was mistakenly added over the step
that we define the `sh' symbolic link, not over the call to patchelf. This
is corrected with this commit.
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After testing the built of Metastore on a server, I noticed that because
its `/etc/passwd' doesn't have the list of users, the `getpwuid' call
within metastore failed and wouldn't let it finish.
So I looked into the code and was able to implement a solution to this
problem by adding two options to it for default values for the user and
group. Also, file attributes are not necessary in our (current) use case of
metastore and caused crashes on our server, so they are also disabled.
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With the current build system, Bash and AWK don't write RPATH into the
executables. This causes many problems in the pipeline (for example when
using the `$(shell)' function in Make which doesn't have
`LD_LIBRARY_PATH').
After consulting the Bash and Make mailing lists, so far, the best solution
was to use the Patchelf program to manually write RPATH in these
executables. With this commit, Patchelf is now installed in the pipeline
and used in Bash and AWK to fix this problem.
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The build of bash has been made a little cleaner to help in readability and
management of the code.
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In the previous commit, the copyright year and owner were mistakenly
modified. They are corrected now.
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While working on a pipeline based on this, I noticed many linking errors of
our installed Bash, complaining that it can't link with libreadline. This
was while readline was present in the proper directory and the Bash within
a recipe would work properly.
After some investigation, I found out that this is because Make's `foreach'
function (which was used to define the targets) was apparently calling Bash
without setting `LD_LIBRARY_PATH', causing this error.
To avoid such sitations, Bash now uses its internal build of readline and
we no longer ask it to link with the installed readline.
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The targets of the links to have the extra common `ncurses' packages were
previously just `pkgconfig/*.pc'! But this would only work when run within
the `installed/lib' directory, not any other! So the targets for these
packages now use an absolute address.
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Wget and cURL depend on many network related libraries by default and if
they are present on the host operating system, they will be linked
with. This causes problems for the pipeline when these libraries are
updated on the host system.
With this commit, I went through the configure time options of both Wget
and cURL and removed any library that didn't seem related to merely
downloading of files (possibly with SSL, because we do build OpenSSL in the
pipeline).
Also, I noticed a new version of cURL has come, so that is also updated.
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In a previous implementation, we were using a `target' variable to define
the final target of several links, but with the new `sov' solution, we just
used its base name. However, we had forgot to correct two instances of
`target'. This is corrected now.
Also, the step to clean all already built outputs of the NCURSES library
has been simplified to a platform independent wildcard.
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On Mac OS systems, the full version number is not used in the filename
given to libncurses. For example for version 6.1, it is called
`libncursesw.6.dylib'. So a more generic and easier to maintain and read
script is now used to be able to make links for both Mac and GNU/Linux
systems.
In short, instead of checking if we are in Mac every time, we just set the
suffixes at the start based on the machine once as variables and use those
to define the links.
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Readline is a prerequisite of Bash and AWK, while NCURSES is a prerequisite
of Readline. With the recent update of GNU Bash (and thus GNU Readline) on
my host operating system, the pipeline crashed and I noticed this hole in
the pipeline. In particular, AWK (which linked with Readline 7.0) would
complain about not finding it and abort.
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ccache is a super annoying program in the context of the reproduction
pipeline. On systems that use it, the `gcc' and `g++' that are found in
PATH are actually calls to `ccache' (so it can manage their call)!
Two steps have been taken to ignore and disable ccache (if it isn't ignored
properly!): 1) when making symbolic links to compilers, if a directory
containing `ccache' is present in the PATH, it is first removed, then we
look for the low-level programs that we won't be building. 2) The
`CCACHE_DISABLE' environment variable is set to 1 where necessary (with the
other environment variables).
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After installing Bash, we would just blindly try to build the $(ibdir)/sh'
symbolic link. But that could fail if it already existed. To make things
clean, we now remove any link first before attempting to make a new one.
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Since the current implementation of this pipeline officially started in
2018, all the files only had 2018 in their copyright years. This has now
been corrected to 2018-2019.
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By giving this option specifically at the build time of Pkg-config, we'll
ensure that any package that uses pkg-config will first look into our
locally installed build.
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Both Gzip and Gnuastro were being bootstrapped personally from their Git
repository until now. But fortunately a new release of both came out last
week and so to make things standard we are now using their standard
tarballs.
I also noticed that we weren't checking the version of Gzip or mentioning
it in the acknowledgement section. This was also corrected.
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While checking the build of the previous commit, a failure happened when
linking `reproduce/build/dependencies/installed/bin/sh' with the built Bash
(because the symbolic link already existed!). So a `-f' flag was added to
`ln' to just change it without complaining.
I also noticed that the Git build was also not in verbose mode. So this has
also been corrected.
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While we were testing this pipeline on a Mac OS system, we found and
reported a problem in Gzip's build (bug #33689). However, since the Gzip
build is not verbose, it was necessary to run its `make' with
`V=1'. Generally, since almost all the programs are built in verbose mode
(where you can see the compilation commands), we have also set this flag in
any build to be clear and make it easier to spot bugs in the future.
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Some problems with using the number of threads in dependency building were
fixed.
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Some host Make systems may not allow automatic passing of the number of
threads to sub-Makes. So while building the basic dependencies, we'll need
to explicity add the `-j' option to the Make files that can benefit most
from it: those that are dependencies of many others (Tar & Make), or are
the last to build (Coreutils).
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The build systems of Libgit2 and WCSLIB on Mac OS does not account for
installation in non-standard addresses: `Libgit2' keeps the absolute
address of its build directory (not the installation directory) and WCSLIB
doesn't write any absolute address at all (so the system uses the first one
it finds).
To address these issues, we are now using Mac OS's `install_name_tool'
program to fix the absolute path within the installed shared library.
Since the version of the library is actually present in its shared library
name, in `dependency-versions.mk' we have also separated these two
libraries so later when their version is changed, we are careful in
correcting the shared library name also.
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`ln' will complain about a link already existing. So to avoid having to
rely on the `-f' option (which may not be portable across systems), when we
are making symbolic links to the OS tools that we won't be building, we now
remove the file if it exists, then make a new symbolic link.
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Until now the low-level links that we put in our internal installation from
the operating system were a prerequisite of essentially all the basic
dependencies. So a change in them would mean a full re-build of all the
basic dependencies. But in building the basic dependencies, we already have
the operating system's PATH and other environment variables. So unlike the
higher-level dependencies, they don't need these links at all!
With this commit, the `low-level-links' file is placed in `installed/bin'
and is a top-level target of the basic dependencies build. In this way, if
it is necessary to update/change to use something from the host operating
system, we can simply delete it and run `./configure' again wihout having
to re-build all the basic dependencies.
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On Mac OS systems, the `sw_vers' executable prints information about the
operating system. It is used by TeX Live to determine the necessary builds
to download and install. We are thus importing it as a low-level tool in
`dependency-basics.mk'.
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Until now, we were checking the existance of the `configure' file and if it
wasn't present, we would check for `config' (for OpenSSL which also has a
lower-level "Configure" script that is called by the `config' script). But
after two tests on Mac machines by Raul Infante Sainz and Cristina Martínez
Lombilla, we found out that Mac Os's file names aren't case sensitive and
thus the build wouldn't use `config', but `Configure'.
Now, the exact configuration script can be specified as the 7th argument to
the `gbuild' script. If it isn't given, the standard `configure' name will
be used, but when it is, the given name will be used.
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OpenSSL can't automatically detect the architecture of Mac OS systems, so
as it suggests on its Wiki, it needs some help for doing that. With this
commit, we are checking the build on Mac OS with the presence of `otool'
(Mac OS's linker). If it's there, we'll add the OpenSSL configuration
options suggested by OpenSSL's Wiki.
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Until now, we weren't including the `rpath' linking options to the basic
dependencies. They are now added. Also, when the download of an input file
fails for any reason, an empty file won't be replaced there any more.
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We were missing a `\' at the end of the `$(call' function of Coreutils to
connect the two lines. It has been fixed now.
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To enable easy downloading of HTTPS links with Wget (this pipeline's defaut
downloader), we need a set of trusted CA certificates. Until the time that
we can generate one ourselves, one generic set of trusted CA certificates
is now downloaded like a tarball and placed in the OpenSSL configuration
directory.
With these CA certificates, within the pipeline we can now safely use the
pipeline's own installed Wget.
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Some high-level programs like Wget and cURL need to be built in shared mode
because they also include dynamic loading of libraries. Therefore, if we
only build the lower-level libraries in static mode, our own build will be
ignored and they will go and find the system's shared libraries to link
with. Because of this, for now, we have manually set the `static_build'
variable in the configure script to `no'.
Also, if the downloader fails, we'll delete the output (an empty file in
the case of Wget) because it interefers with a target definition.
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The TeX Live installer needs Wget to operate smoothly, especially on recent
Mac OS systems that don't have Wget pre-installed. Also, it would be good
for the pipeline to have its own downloader. So with this commit, the
pipeline also installs Wget and OpenSSL which is a dependency.
Many other small changes/fixes were done in this process.
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The main reason I wasn't using cURL as a downloading tool was that I wasn't
familar with how to ask it to follow a re-direct. But I just found out that
its with the `-L' configure time option. So it is now added as a downloader
tool to the pipeline.
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GNU Binutils (which provides the GNU Linker) is not ported to Mac OS
systems. GCC also takes a very long time to build, and if we are to still
have linking problems with LLVM's linker, it would be better to just ignore
GCC also and use the system's C compiler and linker together.
So for the time being, GCC isn't a main target of the basic dependencies
and won't be installed. But we have kept the rules that were checked on a
GNU/Linux operating system.
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The pipeline now installs GCC and all its necessary prerequisites.
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The linker of LLVM version 10.0.0 (clang-1000.11.45.5) doesn't recognize
the `-rpath' linker option! After some searching, apparently it does
recognize `-rpath-link' so we are testing with that now.
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Until now we weren't explicity writing the full path of the dynamic
libraries necessary for linking a program. But now with
`-Wl,-rpath=$(ildir)' we ensure that the linker keeps the address of the
dynamic libraries necessary for linking at linking time, not running
time. Also, `pkg-config' is also built when preparing the basics. Several
other minor corrections were made thanks to the great help of Raúl Infante
Sainz.
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The high-level dependencies are now built without having access to the
system's PATH. To do this, all the necessary software that we aren't
building ourselves are now brought into the installed `bin/' directory
using a symbolic link to the corresponding software on the host. To do
this, it was also necessary to increase the number of basic/low-level
packages that we are building, and add several more (Diffutils and
Findutils).
With this process in place, we now have a list of the exact software
packages that we are not building our selves, enabling easy building of all
such dependencies in the future.
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While working on a research project using this pipeline, I noticed that we
don't have any `sh' executable within our PATH. However, some programs
(including Gnuastro's configure script, when it is checking for shells to
use with Libtool) check and use it. So after building Bash, we also build
an `sh' symbolic link to point to the built Bash executable.
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The system's libraries are no longer used in building the higher-level
dependencies. Also, thanks to Raul Infante Sainz, we found out that Bash's
build script was still removing the extra directory information (not
good!).
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GNU Coreutils are basic programs that can help in the configuration of
higher-level programs. Because of that, it was a dependency of almost all
software built in `dependencies.mk'. To make things more clear, easier to
read and faster (when building in parallel), the building of Coreutils is
now moved to the `dependencies-basic.mk' rules. There, it is built
along-side Bash. Since `dependenceis-basic.mk' is run and completed before
`dependencies.mk', with this, we can be sure that Coreutils is present by
the time we want to build the higher-level programs.
Also, Zlib is now added as a dependency of Git also (it is necessary for
its build).
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When the C compiler is not GNU GCC, linking with GNU Binutils is going to
cause problems. So until the time that we can include GCC into this
pipeline, its best to avoid Binutils also.
Also, for building CMake, we were relying on an installed CMake, but now,
we are using its own `./bootstrap' script, so it can be built even if the
host system doesn't have CMake.
Also, for TeX Live, we are now setting a custom file as main target to
avoid complications with symbolic links as targets in Make.
Finally, when the user says they don't want to re-write an existing
configuration file, no extra notices will be printed and the configure
script will immediately start building programs.
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Until now, we were using a customized `tar.lz' tarball for Gzip. But on
systems that don't have GNU Tar, this will cause a problem (non-GNU Tar
doesn't recognize `.tar.lz'). So to keep things simple, we are using the
customized gzip in `tar.gz' format. After the internal build of GNU Tar and
Lzip, the default method of unpacking (`tar xf XXXXX.tar.XX') will work
nicely on all the standard compression algorithms and we don't have to
modify our commands based on the algorithm (nice feature of GNU Tar).
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Since the final product of the pipeline is a LaTeX-created PDF file, it was
necessary to also have LaTeX within the pipeline. With this commit, TeX
Live is also built as part of the configuration and all the necessary
packages to build the PDF are also installed and mentioned in the paper
along with their versions.
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The default Mac compiler has problems building static libraries. Since we
are not yet building the GNU C Compiler as part of the pipeline, we'll have
to rely on the host system's compiler. Therefore, a check is now added a
the start of the configure script that will build a minimal program with
the `-static' flag and if it fails, it will print a warning. Afterwards,
none of the dependencies will be built with the `-static' flag.
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A semi-colon was missed in defining the link for `zlib'. It is now added.
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To have better control over the build, GNU Binutils, Bzip2, GNU Gzip, and
XZ Utils have also been added to the pipeline. Some other minor cleanups
and fixes were also implemented throughout the process.
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Until now, when a package was to be built statically, we were adding the
`--static' option to `CFLAGS'. This was the wrong place to put it! It
should be in the linking step (thus `LDFLAGS'). Also, based on Bash's
configure script, we are now using the more generic form of `-static'
(single dash, not double dash).
On the other hand, the `--disable-shared' option isn't available in many of
the packages and it is highly redundant with the `-static' option, so it
has been removed to avoid an extra warning in such packages.
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To ensure the easy unpacking and building of the programs, Lzip and Tar are
now also build during the initial setup phase.
Some minor corrections were also applied to make things cleaner and
smoother.
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