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Until this commit, the addion of `-liconv' to `CXXFLAGS' in `high-level.mk'
dependend on `host_cc', but I had forgot that `host_cc' isn't defined for
`high-level.mk'. It is now defined for this Makefile also in the configure
script.
Also, the Standard C++ library depends on `libgcc_s.so.1', so after
building GCC, it was necessary to add Rpath to it.
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While doing a clean build, several issues were found in the pipeline and
corrected. The main issue was that with the recent installation of
`libiconv', the GCC standard C++ library depends on `libiconv', so we need
to explicity add an `-liconv' to any C++ compilation.
The other corrected points are:
- The C++ compiler is now explicitly defined in `CXX'.
- libgit2 and WCSLIB's recipes weren't using `&&' between statements, so
if there was an error, it would still build the target!
- The CMake bootstrapping script now builds much faster in parallel.
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While testing on a system with no Texinfo, we noticed that M4 depends on
Texinfo. To fix this problem, with this commit, it is now included in the
pipeline.
While doing a clean build, a few minor issues were also found and corrected
in the other rules.
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Until now, we were using the `--enable-single' configure-time option of
FFTW to build its single-precision library. The reason was that according
to the output of `./configure --help', this was equivalent to
`--enable-float'. However, the single precision library wasn't being built.
As a result, on systems that already had it, SExtractor would use the
system's library and on other systems, it would simply not pass the
configure step.
With this commit, we are now using `--enable-float' which fixes this
problem and installs the `libfftw3f*' libraries (showing that it is not
equal to `--enable-single'!). Also, some optimization flags were added to
hopefully make it faster.
This issue was found thanks to Zahra Sharbaf and Hamed Altafi.
This fixes bug #56588.
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Until now, we were letting the TeXLive installer use the default
CTAN-chosen mirror based on the host. But in many cases, this is not
efficient and sometimes those servers don't work.
With this commit, we manually set the server to use (`rit.edu'), which is
relatively fast and up to date. In this way, until we build TeXLive from
source, every user will be using the same CTAN mirror.
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On some Fedora systems, Wget's build conflicts with libiconv.
With this commit, we use Wget's `--without-libiconv-prefix' configure
option so it will be built without an outside libiconv.
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On some Fedora systems, libffi installs under `lib64', not `lib'. As a
result, Python's Setuptools can't find it and will not built (complaining
about not finding the `_ctypes' module).
With this commit, we fix this problem by explicitly putting a copy of
libffi's installed libraries within the `lib' directory.
This issue was found while testing the pipeline with Elham Saremi and Hamed
Altafi.
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Until now, we weren't explicitly setting the C and Fortran compiler
environment variables (`CC' and `F77'). As a result, if the user's system
had already set them, there would be a problem (and the system's compilers
would be used).
With this commit, we are explicitly setting these two environment variables
at the start of `high-level.mk'.
This bug was found after a discussion with Elham Saremi.
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An existing `libiconv' can cause a conflict with `pkg-config', this is why
`libiconv' depends on `pkg-config'. On a clean build, `pkg-config' is built
first. But when we don't have a clean build (and `libiconv' exists) there
will be a problem.
With this commit, before re-building `pkg-config', we'll remove any
possibly existing installation of `libiconv'.
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There was only a conflict with `.file-metadata'.
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While reviewing Prasenjit's commits, I noticed that we had forgot to add
the citation for TIDES, also to make things clear, the program/library
build rules are now sorted alphabetically.
Finally, I noticed that after building the TiKZ PDF figures, it is crashing
(like on Prasenjit's computer). After looking around, I noticed its because
we were setting the of the `TEXINPUTS' environment variable to be the
installed TeX Live directory (which was ultimately redundant because by
default TeX will look into where it was installed). The important thing is
just that we remove any possible value the host system has, not to set new
directories.
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Libiconv has to be installed before pkg-config otherwise there
would be a compilation error:
gconvert.c:61:2: error: #error GNU libiconv not in use but included
iconv.h is from libiconv
61 | #error GNU libiconv not in use but included iconv.h is from
libiconv
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TIDES is an ODE integrator with multiple-precision arithmetic.
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Several corrections were necessary in the basic build: 1) the
version of GCC on some systems includes an `_' which would cause
a crash when building the PDF. 2) libcharset had to be manually
added to the Git build.
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Prasenjit Saha reported that while building on a macOS, Git complained
about not finding `libiconv' functions. Therefore with this commit,
`libiconv' is also built as a dependency of Git.
Also, since the build of Binutils (and the subsequent GCC) doesn't depend
on the exact versions of the other basic software, they are set as
existance-only prerequsites (ignoring their timestamps). This is done to
avoid re-building when it is not needed.
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The comment above Gnuastro's build rule is not longer relevant, so it has
been removed.
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Until now, on GNU/Linux systems, GNU Binutils was built in parallel with
other programs. As a result, the moment that the Binutils executables (most
importantly `ld') are being installed, if another program is using them, we
can have a crash.
For some reason, this crash doesn't happen on Fedora or Arch Linux, but on
some Debian-based distors, it causes the following crash when we are
building Git (which happened to be built while Binuntils is being
installed):
credential-cache--daemon.o: file not recognized: File format not recognized
In a following run of `./configure' (when Binutils has been installed), Git
will build and install successfully.
To fix this problem, with this commit, all basic programs are now a
prerequisite of Binutils and Binutils is the sole prerequisite of GCC
(which is the final target of `basic.mk').
Also, the GCC configure options were re-ordered to be easier to read (the
`--with-*' options under each other, the `--enable-*' options under each
other and so on).
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Until now we hadn't noticed that Metastore's build doesn't include an
`rpath'. As a result I got a crash during a Git commit.
With this commit, on GNU/Linux systems, we now add rpath to the installed
Metastore executable. During the build, I also cleaned up the Metastore
build recipe to be more clear and readable (in particular we only check the
user name and group name when metastore is actually built).
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The recent work by Raul to import Imfit is now merged into the master
branch. Only a few minor conflicts came up due to the update with CFITSIO
(that Raul also done in parallel on this branch).
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While trying to debug the installation of Imfit, we found out
that libcurl doesn't have rpath and is thus linking with the
host system's libraries. So rpath is now manually added to the
build of libcurl. We also found out that Imfit executables
don't have rpath, so it was added to them too.
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Until now, TeXlive would only attempt to download/update LaTeX packages,
but after some time, it will be necessary for it to update itself. When
this happens, it complains about running it with `update --self'.
To fix this problem, before installing/updating the LaTeX packages, we will
first update tlmgr in any case.
Also, we weren't removing the TeXlive package version file before appending
the values to it. So it was just repeating the packages every time it was
updated. With this commit, it is being removed on every new build.
Finally, the version of Git was updated to its most recent version.
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Until this commit, 'imfit' was installed using proper flags in order to
use our own libraries. However, it looks first of all to the default
system. As a consecuence, `imfit' program was linked to the host system
libraries, even when we told to use our own libraries!!
With this commit, the installation of `imfit' has been modified in order
to remove the default paths already set in the `SConstruct' script. By
doing this, only our paths are take into account for compiling the
program. It has been tested on Mac OS laptop and it works fine. Test on
GNU/Linux systems remain before merge into the main project branch.
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Until this commit, `fftw' was building single precission float library
because `scamp' had problem on using the default double precission
library. However,`imfit' and maybe other programs will use double
precission float libraries.
With this commit, `fftw' installation is done twice in order to build
single and double precission float libraries. It does not complain and
goes up to the end without crashing. However, more tests are needed in
order to ensure that there is not problem on having both libraries
because in principle, they share the same header file and that could
cause problems.
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`cfitsio' was recently updated and it cames up with a problem when
trying to build shared libraries (on Mac OS system laptop). This is
because the `configure' script for building `cfitsio' include by default
`rpath'.
With this commit, this issue is fixed by modifying the installation of
`cfitsio'. Using `sed', each ocurrence of `@rpath' in `configure' is
replaced by `$(ildir)'. Once it has been done, the installation of
`cfitsio' goes as normal.
In this commit, the version of the `cfitsio' has been also updated to
the most recent one.
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With this commit, I have corrected a typo in the installation of
`imfit'. In principle it is working on Mac OS system but when I tried to
install it in GNU/Linux system it crashed. It complains about a problem
with the `cfitsio' library:
/pathto/libcfitsio.a: error adding symbols: File format not recognized
As in the last commits done by Mohammad in the project, `cfitsio'
installation has been upgraded and also the installation has been
modified, I am going to try this new version. I will also check if it is
a problem about dynamic/static library.
It also seems that the installation is taking libraries and variables
from the host system, so I will check that everything used is from our
own programs/libraries.
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Until now, CFITSIO had several peculiar features which needed special
attention: 1) Its tarball didn't have a `.' in the version name and would
sometimes have extra `0's. 2) When unpacked it was just `cfitsio'. 3) It
hard coded the directory to search for cURL library. All of these forced us
to do a lot of extra steps for CFITSIO.
So I got in touch with them and fortunately they were very open to
correcting these issues and with version 3.47 all such issues have been
addressed in the tarball. Thanks to these changes, with this commit,
CFITSIO's build rule is now very similar to many other programs.
I also noticed that it has an optional `--with-bz2' feature to enable
unpacking `.fits.bz2' files. So this feature is also added.
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Until this commit, `imfit' paper was not included into the
acknowledgements.
With this commit, a bib tex file for `imfit' has been added. So, now it
is properly cited into the final paper.
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With this commit, `imfit' has been included into the project. As described
in the official webpage (http://www.mpe.mpg.de/~erwin/code/imfit/):
Imfit is a program for fitting astronomical images -- especially images
of galaxies, though it can in principle be used for fitting other
sources.
This program uses the `scons' program to build itself (not the traditional
GNU `configure' and `make' system). I have tested it by using an example
that can be found in the `examples' directory of the decompressed
tarball. It works fine without any error on my Mac OS system.
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With this commit, SCons has been included into the project. As in the
official webpage of this program says:
SCons is an Open Source software construction tool—that is, a
next-generation build tool. Think of SCons as an improved,
cross-platform substitute for the classic Make utility with integrated
functionality similar to autoconf/automake and compiler caches such as
ccache. In short, SCons is an easier, more reliable and faster way to
build software.
The motivation for including this software into the project is because
there are some software that use this system for the installation. In
particular, the necessity of installing it comes from Imfit. This is an
astronomical software that uses this system so that is why it has been
included into the project. In principle it is simple, and I have tested
it on Mac OS sytem without any problem.
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Until this commit, the name of the decompressed tarball directory of
PyYAML Python package was wrong. It has to be `PyYAML-version' instead
of `pyyaml-version'. When I run the installation on Mac OS system it
went up to the end of the installation with no error. However, when I
tried to install it on a GNU/Linux system, it complained about no
finding the `pyyaml-version' directory, which is the expected because
the name was wrong!
With this commit, I have fixed this issue by writting correctly the name
of the decompressed tarball directory.
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With this commit, PyYAML Python package has been added into the project.
It is widely used in the Python community and the goal is to have human
readable configuration files. As in the web page
(https://pypi.org/project/PyYAML/) says:
YAML is a data serialization format designed for human readability and
interaction with scripting languages. PyYAML is a YAML parser and
emitter for Python.
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With this commit, LibYAML library has been added. This library is a
prerequisite of the Python package PyYAML, which is widely used in the
Python community when configuration scripts are needed.
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By default (when you run `make' within CFITSIO), it only builds a static
library. So until now, the template would only install a static version of
this library.
To be more clear about which libraries are used during the linking of
programs that use CFITSIO, it would be helpful to have shared library
versions also. Also, if the system has problems with static libraries (like
macOS systems), then it won't go looking outside the template to link with
them (these paths are hardcoded in the linker, which we don't build on
macOS and just use the system's tools).
With this commit, we are explicity running `make shared' in the CFITSIO
installation to have shared CFITSIO also. I also removed the old `static'
element (which we don't use anymore in any of the programs and have to
remove some time later!).
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Matplotlib can optionally use LaTeX and Ghostscript as dependencies to
render text with LaTeX.
Since we already have their build rules, with this commit, they have been
added as its prerequisites.
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With this commit, ImageMagick program has been set as prerequisite of
Matplotlib Python package. Since some submodules of Matplotlib rely on
ImageMagick programs (for example, those to make image animations), and
now we have ImageMagick into the project, it is good to install
ImageMagick when Matplotlib is requested to be installed.
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With this commit, ImageMagick software has been added into the project.
This software is useful to deal and treat images from the command line.
Since it is widely used and a lot of other programs rely on it, it is
worth to have it into the project.
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In the previous commits where Metastore's recipe was updated, all the
`TAB's in the recipe were saved as spaces just before the commit (due to a
copying and pasting from the terminal, not the text editor). With this
commit, I am correcting this.
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Until now, in the recipe to build Metastore, we would store the current
directory in a `current_dir' Bash variable before running `gbuild' to build
Metastore. However, in this Makefile, we aren't using `.ONESHELL'. As a
result, each un-quoted new-line character creates a new shell and the
`current_dir' variable that we used afterwards was empty!
This happened because until recently, Metastore was being built in
`high-level.mk' (where `.ONESHELL' is activated, because we are using GNU
Make to call that Makefile). But in `basic.mk', we are using the host's
Make, which may not be GNU Make, so we can't use any GNU-only features.
Also, this error was hard to notice, because we weren't using `&&' before
writing the final target of Metastore!
With this commit, both this issues are addressed: all the lines in the
recipe are now quoted in the end with a backslash, and the steps before
making the target are separated by `&&', not `;' (which doesn't cause a
crash if the command fails).
This fixes bug #56295.
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Until this commit, Binutils was brough up as a GCC prerequisite two times:
Once as a special (`host_cc') dependency (for when we want to build GCC),
another time as a dependency in every build. The first one is now obsolete:
on MacOS systems where we don't build Binutils, we define its symbolic
links in the same recipe.
With this commit, we remove the first one, so Binutils is always a
dependency of GCC.
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In the warnings output by LaTeX during the building of a project, I noticed
that `csquotes' is recommended for some features of BibLaTeX (a warning was
printed) so it is added with this commit.
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There weren't any conflicts in this merge.
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Until this commit, we were installing `netpbm' without disabling the X
Windows System in GNU/Linux. That is the default option in the configure
step of `netpbm'. However, we are not installing the necessary libraries
(X11) and headers for that. As a consecuence, when testing in a system
where we don't have these libraries/headers (Ubuntu 14.04), it crashes.
With this commit, we disable the X Windows System option in `netpbm' by
giving the answer `none' to one of the last answers to that question in
the configure step.
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Until now the software names and versions in
`reproduce/software/config/installation/versions.mk' were placed such that
all the versions were placed under each other. This had a visual effect,
but since many of the software have shorter names, it could sometimes cause
visual confusion on which number belongs to which software.
Since we recently removed a similar situation with the backslashes, with
this commit, there is only a single space between the variable name, `='
and the version number.
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GCC 9.1 was just released and includes many new optimization features that
can benefit projects in this template also.
Also, the build directory of GCC has been moved inside the unpacked
directory (similar to all the other programs). As a result, while GCC is
being built, the `.build/software/build-tmp' directory will only have one
directory for GCC. Until now, there was one `gcc-build' directory and one
unpacked tarball.
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Since we just download the binary source of TeXLive, we need to keep it up
to date with the server. So it has been incremented to 2019 (TeXLive 2019
was released April 29th).
A note was also added in the Checklist to keep the users informed on how to
update TeXLive if necessary.
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Until this commit, we were installing `cairo' without disabling the X
Windows System. That is the default option in the configure step of
`cairo'. However, we are not installing the necessaries libraries (X11)
and headers for that. As a consecuence, when testing in a system where
we don't have these libraries/headers (Ubuntu 14.04), it crashes.
With this commit, we disable the X Windows System option in `cairo'
configure step by setting the option `--with-x=no'.
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In the last imported work about fixing all backslashes, the extension of
`netpbm' tarball was not the correct one. Now we are using `.tar.gz'
instead of `.tgz'.
With this commit, we fix this typo by replacing the `.tgz' by `.tar.gz'
in the rule of `netpbm'.
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In the recent correction of backslashes, I had missed adding an `&&' before
the `rm' command of the generic CMake building rule (`cbuild' of
`build-rules.mk'). With this commit, this has been corrected.
A multi-threaded Make was also added to build OpenMPI (which takes long and
is often built alone because it takes so long and other things depend on
it) and the HDF5 library.
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The TAB character wasn't used in the second line of the recipe to build
SCAMP. This has been corrected with this commit.
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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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