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It was some time since these three software were not updated! With this
commit the template now uses the most recent stable release of these
packages.
Also, the hosting server for ImageMagick was moved to my own webpage
because unfortunately ImageMagick removes its tarballs from its own
version.
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Until now we were calling it `Sextractor', but the official way of writing
it is `SExtractor'. With this commit, this has been corrected.
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Until now, we were assuming that the users would just clone the project in
Git. But after submitting arXiv:1909.11230, and trying to build directly
from the arXiv source, I noticed several problems that wouldn't allow users
to build it automatically. So I tried the build step by step and was able
to find a fix for the several issues that came up.
The scripting parts of the fix were primarily related to the fact that the
unpacked arXiv tarball isn't under version control, so some checks had to
be put there. Also, we wanted to make it easy to remove the extra files, so
an extra `--clean-texdit' option was added to `./project'.
Finally, some manual corrections were necessary (prior to running
`./project', which are now described in `README.md'. Most of the later
steps can be automated and we should do it later, I just don't have enough
time now.
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New versions of astropy, bash, cmake, curl, findutils, gawk, gcc,
ghostscript, git, make, gsl had recently come so they are updated with this
commit.
About GNU Findutils and GNU Make: I was bootstrapping (building the tarball
of) these two separately separately because their standard tarball release
had problems on some systems. Both have been updated now so I am no longer
using my own webpage as their main URL.
A special note about GNU Make. I just noticed that during bootstrapping,
GNU Make would use the fixed version string of `4.2.90' for any commit!!!
But fortunately they have officially released their 4.2.90 version, so we
are safely using their own webpage. The only difference is the compression
format. My old bootstrapped build was `tar.lz', but the standard release is
`tar.gz'.
Also, all the basic programs (installed in `.local/bin') in `basic.mk' are
now existance-only dependencies (after a `|'). Because later programs just
use them at a very basic level, so there is no need to rebuild everything
when Bash gets updated for example.
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Until now, OpenMPI would complain about not having `ssh' or `rsh' as a
remote shell feature. However, such features should not be necessary in a
reproducible scenario and they also have major security issues.
With this commit, we are now using OpenMPI's `OMPI_MCA_plm_rsh_agent'
environment variable to disable any remote shell dependency for it (as
suggested by Boud). Therefore, any dependency for OpenSSH has been
removed. But I thought to keep the build instructions incase it may be
useful under some un-foreseen scenario. However, to discourage people from
building it, a notice was added ontop of the build instructions.
This bug was found, tested and solved thanks to Roberto Baena Gallé and
Boud Roukema.
This fixes bug #56724.
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Until now we have followed the convention of using space characters before
comment lines in recepies, not tabs. This has been corrected in one case.
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Until this commit, `fpack' and `funpack' were not installed by default
with the installation of CFITSIO. It is necessary to explicity do a
`make fpack' and `make funpack' to have them installed. With this
commit, these two programs have been added.
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Until this commit, the name of the variable for `beautifulsoup4'
checksum was wrong, and because of that, it was not able to install it.
With this commit, `beautifulsoup-checksum' has been replaced for
`beautifulsoup4-checksum' in the `reproduce/software/make/python.mk'
Makefile, and the problem has been fixed. This was not noticed
previously because this Python package is only installed when some high
level programs are requested to be installed.
With this commit the version of `imagemagick' program has been also
updated because the previous version is not available in the official
website anymore.
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When trying to install `libgit2' on my macOS system, it complains about
not finding `_iconv*' functions! But apparently `libgit2' has its own
implementation of `libiconv' that it uses if it can't find `libiconv' on
macOS. So, the solution to this problem was to add `-DUSE_ICONV=OFF' to
the configuration options of `libgit2'.
I reported this issue that now is fixed thanks to the help of Mohammad
Akhlaghi.
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Until now, we weren't explicitly telling libtiff to ignore JBIG-KIT. So on
some systems, it would try to link withit and would thus fail.
With this commit, we have disabled JBIG-KIT support for libtiff. I tried to
import it into the template, but it doesn't have use the standard GNU Build
system. Maybe later we can add a set of build rules for it, I don't have
time now.
Also, this problem with libtiff occurred while building Ghostscript. But
was fixed after adding this option to libtiff. So libtiff was added as a
dependency of Ghostscript.
This bug was reported by Sheeraz Ahmad.
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Until now we weren't setting OpenSSH's `privsep-path' configure option. As
a result, it would try to use its default (`/var/empty'). Therefore, when
the host doesn't have `/var/empty', OpenSSH would crash because of not
having permissions to create this directory.
With this commit, we are now using OpenSSH's `--with-privsep-path'
configure-time option to explicitly use a directory with the project's
build directory.
This bug was found by Sheeraz Ahmad and Amina Aahil.
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This was a bug in WCSLIB 6.3 that has been fixed in WCSLIB 6.4. From
WCSLIB's changelog: "The rule change to the Fortran makefile in v6.3 to add
getwcstab_f.o to the sharable library causes it to depend on CFITSIO to
resolve fits_get_wcstab(). Hence backed out of that change.".
The actual error was like this:
Undefined symbols for architecture x86_64:
"_fits_read_wcstab", referenced from:
_ftwcst_ in getwcstab_f.o
"_gFitsFiles", referenced from:
_ftwcst_ in getwcstab_f.o
ld: symbol(s) not found for architecture x86_64
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These three libraries are dependencies of Biber, so we will need them
later, but since we don't build biber from source now, we can't control
what library it links with. With this commit, we have just added their
versions, checksum, download URL and build rule incase they are useful in
other software.
Later, when we build Biber (and Texlive in general) from source, we'll be
able to use these.
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In the line where we checked if libffi is installed in `lib/' or `lib64/',
there was a typo that lead to an incorrect result: we had forgot to add a
`-f' to the second check. This is corrected with this commit.
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Until now, unlike most other programs, in Gnuastro we would run `make
check', but this causes a crash on some systems, because of its
BuildProgram test: a linking error because the library isn't installed
yet. Which is natural in cases like this (and must be corrected in future
Gnuastro releases).
With this commit, the checks of Gnuastro have been removed.
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Until now, when building PatchELF, we would always require that it be done
statically. However, some systems don't have a static C library available
for linking. This cause a crash in the static building of PatchELF. But a
static PatchELF is necessary for correcting RPATH in GCC's outputs.
With this commit, in the configure script we check if a static C library is
linkable for the compiler. If it isn't then `host_cc' will be set to 1 and
GCC won't be built. We also pass the result of this test to `basic.mk'
(through `good_static_lib'), so if a static C library isn't available, it
builds a dynamically linked PatchELF.
This bug was reported by Elham Saremi.
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Until now, OpenMPI was being installed without any dependency. This was
fine because it would indeed build. But the moment you tried loading
something that depends on it (for example `mpi4py' through `astropy'), you
would get an error complaining that SSH isn't present.
With this commit, the pipeline now also installs OpenSSH to solve this
problem.
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Until now, we were relying on WCSLIB's internal checking and linking with
CFITSIO. But on one macOS system (not others that had no problem!), we
noticed that it complains with undefined symbol linking errors to CFITSIO
libraries.
With this commit, as a fast/ugly solution, we are explicity adding
`-lcfitsio' to WCSLIB's `LIBS' variable so all binaries are linked with it
automatically. We'll be in touch with the WCSLIB author to see if a better
solution can be found.
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Until now, we weren't explicitly disabling Java in the build of libffi
because there was no Java platform on the systems we tested. But recently
Yahya Sefidbakht report a crash in libffi (reported in bug #56716) because
of Java not being compiled properly.
Unfortunately libffi doesn't have a configure option to disable Java, but
it does have an internal macro (`NO_JAVA_RAW_API'). With this commit, we
we defined this macro in the `make' step, and it solved the problem.
This fixes bug #56716.
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Some of the software tarballs are directly available on their webpage (for
example due to build problems on systems, where we had to clone the
software and build its tarball ourselves until the next release). Until
now, only for these software, these tarballs were hosted on
`http://akhlaghi.org/src'. But now, I have moved a clone of the software
backup repository (including all its software) to
`http://akhlaghi.org/reproduce-software'.
To be more clear and have a single place for the backup software, the URL
of those software has also been updated in the project source.
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Until now, in version 3.0.1, mpi4py couldn't be built with the most recent
version of OpenMPI. However, after trying the next version (3.0.2), I
noticed that it builds successfully without a problem.
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After making the previous commit, I noticed an extra line (redundantly
defining a wrong `BASH_ENV') that should have been deleted. It has been
corrected.
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Until now the only way to define the environment of the Make recipes was
through the exported Make variables (mostly in `initialize.mk' for the
analysis steps for example). However, there is only so much you can do with
environment variables! In some situations you want slightly more
complicated environment control, like setting an alias or running of
scripts (things that are commonly done in the `~/.bashrc' file of users to
configure their interactive, non-login shells).
With this commit, a `reproduce/software/bash/bashrc.sh' has been defined
for this job (which is currently empty!). Every major Make step of the
project adds this file as the `BASH_ENV' environment variable, so the shell
that is created to execute a recipe first executes this file, then the
recipe. Each top-level Makefile also defines a `PROJECT_STATUS' environment
variable that enables users to limit their envirnoment setup based on the
condition it is being setup (in particular in the early phase of
`basic.mk', where the user can't make any assumption about the programs and
has to write a portable shell script).
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After adding the libiconv library to the template, the C++ library uses
three of its functions (`libiconv', `libiconv_open' and
`libiconv_close'). However, it doesn't explicity link with it inside its
shared library!
I tried by exporting `LIBS=-liconv' before the GCC configure script but it
crashed as soon as it went on to the second GCC building stage (because
this environment variable was no longer present there). I also tried adding
the C++ configure option of `--enable-cstdio' to the GCC configure options
(so it doesn't use iconv according to the manual), but it made no change.
With this commit, as a brute-force solution, `patchelf --add-needed' is run
on the installed `libstdc++.so', so `libiconv.so' is explicitly included
inside the `libstdc++' shared library.
This bug was found by Roberto Baena Galle while trying to load Matplotlib
(which needed the C++ library).
This fixes bug #56702.
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Until now, there was no check on the integrity of the contents of the
downloaded/copied software tarballs, we only relied on the tarball
name. This could be bad for reproducibility and security, for example on
one server the name of a tarball may be the same but with different
content.
With this commit, the SHA512 checksums of all the software are stored in
the newly created `checksums.mk' (similar to how the versions are stored in
the `versions.mk'). The resulting variable is then defined for each
software and after downloading/copying the file we check to see if the new
tarball has the same checksum as the stored value. If it doesn't the script
will crash with an error, informing the user of the problem.
The only limitation now is a bootstrapping problem: if the host system
doesn't already an `sha512sum' executable, we will not do any checksum
verification until we install our `sha512sum' (as part of GNU
Coreutils). All the tarballs downloaded after GNU Coreutils are built will
have their checksums validated. By default almost all GNU/Linux systems
will have a usable `sha512sum' (its part of GNU Coreutils after all for a
long time: from the Coreutils Changelog file atleast since 2013).
This completes task #15347.
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Until now, to work on a project, it was necessary to `./configure' it and
build the software. Then we had to run `.local/bin/make' to run the project
and do the analysis every time. If the project was a shared project between
many users on a large server, it was necessary to call the `./for-group'
script.
This way of managing the project had a major problem: since the user
directly called the lower-level `./configure' or `.local/bin/make' it was
not possible to provide high-level control (for example limiting the
environment variables). This was especially noticed recently with a bug
that was related to environment variables (bug #56682).
With this commit, this problem is solved using a single script called
`project' in the top directory. To configure and build the project, users
can now run these commands:
$ ./project configure
$ ./project make
To work on the project with other users in a group these commands can be
used:
$ ./project configure --group=GROUPNAME
$ ./project make --group=GROUPNAME
The old options to both configure and make the project are still valid. Run
`./project --help' to see a list. For example:
$ ./project configure -e --host-cc
$ ./project make -j8
The old `configure' script has been moved to
`reproduce/software/bash/configure.sh' and is called by the new `./project'
script. The `./project' script now just manages the options, then passes
control to the `configure.sh' script. For the "make" step, it also reads
the options, then calls Make. So in the lower-level nothing has
changed. Only the `./project' script is now the single/direct user
interface of the project.
On a parallel note: as part of bug #56682, we also found out that on some
macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set
to blank. This is no problem because RPATH is automatically set in macOS
and the executables and libraries contain the absolute address of the
libraries they should link with. But having `DYLD_LIBRARY_PATH' can
conflict with some low-level system libraries and cause very hard to debug
linking errors (like that reported in the bug report).
This fixes bug #56682.
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Until now we were only setting the `LD_LIBRARY_PATH' environment variable
for GNU/Linux systems. But macOS systems use the `DYLD_LIBRARY_PATH'.
With this commit, for better control over the environment, we are also
fixing `DYLD_LIBRARY_PATH' in all the places that we are setting the
general environment variables.
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Until now, like all other software, PatchELF would install with dynamic
linking. However, PatchELF links with `libstdc++' so on one system, I
noticed that PatchELF gives a segmentation fault and corrupts `libstdc++'
while correcting its RPATH (after installing GCC). The solution is to build
PatchELF statically.
With this commit, we force PatchELF to be built statically (it only
installs on GNU/Linux systems anyway, so there is no problem with static
linking on macOS). This solved the problem on that system.
While looking at its documentation, I also noticed that a new version of
PatchELF has been released after almost three years, so it has been updated
in the template also.
This fixes bug #56673.
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Some bugs have been fixed in the new version of WCSLIB, so it has been
updated in the template.
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More than two releases and bug fixes have been made to libgit2. So we are
now using a more recent version in the template.
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Configure script: when `texlive-ready-tlmgr' is not created, it is similar
to not having installed TeXLive. A check was added so in this scenario the
`./configure' script doesn't crash.
high-level.mk: `cairo' and `pixman' are now installed in parallel and with
`V=1' (so the full compilation and linking command is printed).
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In one of the last few commits, the commands in the recipe of libgit2 was
merged with `&&' so it stops if anything fails. But I had forgot to add a
`;' at the end of the `install_name_tool' command. This is corrected with
this commit.
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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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