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One of the main reasons to building Maneage is to properly
acknowledge/attribute the authors of software in research. So we have
adopted a standard of never referring to the GNU-based operating systems
running the Linux kernel simply as "Linux", we avoid terms like "Open
Sourse" and use Free Software instead (in the same spirit).
With this commit, a few instances of the cases above have been corrected,
they had slipped through our fingers when we initially imported them into
the project. In the special case of the "Journal for Open Source Software",
we simply replaced it with its abbreviation (JOSS). This was done because
in effect we were generally using journal name abbreviations in almost all
the citations already. To avoid any inconsistancies, the names of the three
other journals that weren't abbreviated are also abbreviated.
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With this commit, Maneage now includes instructions to build the memory
tracing tool Valgrind and the program 'patch' (to apply corrections/patches
in text files and in particular the sources of programs).
For this version of Valgrind, some patches were necessary for an interface
with OpenMPI 2.x (which is the case now). Also note that this version of
Valgrind's checks can fail with GCC 10.1.x (when using '--host-cc'), and
the failures aren't due to internal problems but due to how the tests are
designed (https://bugs.gentoo.org/707598). So currently if any of
Valgrind's checks fail, Maneage still assumes that Valgrind was built and
installed successfully.
While testing on macOS, we noticed that it needs the macOS-specific 'mig'
program which we can't build in Maneage. DESCRIPTION: The mig command
invokes the Mach Interface Generator to generate Remote Procedure Call
(RPC) code for client-server style Mach IPC from specification files. So a
symbolic link to the system's 'mig' is now added to the project's programs
on macOS systems.
This commit's build of Patch and Valgrind has been tested on two GNU/Linux
distributions (Debian and ArchLinux) as well as macOS.
Work on this commit started by Boud Roukema, but also involved tests and
corrections by Mohammad Akhlaghi and Raul Infante-Sainz.
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In time, some of the copyright license description had been mistakenly
shortened to two paragraphs instead of the original three that is
recommended in the GPL. With this commit, they are corrected to be exactly
in the same three paragraph format suggested by GPL.
The following files also didn't have a copyright notice, so one was added
for them:
reproduce/software/make/README.md
reproduce/software/bibtex/healpix.tex
reproduce/analysis/config/delete-me-num.conf
reproduce/analysis/config/verify-outputs.conf
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Until this commit, Scamp was installed with the option
`--enable-plplot=yes' (the default). However, Maneage does not have PLplot
included. As it is possible to install Scamp without PLplot (in that case
it won't generate plots), with this commit this option has been set to
`no'. As a consequence, Scamp will be installed even if the host system
does not have PLplot without crashing (but it won't make any plot).
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Until now Maneage used the host's GNU Gettext if it was present. Gettext is
a relatively low-level software that enables programs to print messages in
different languages based on the host environment. Even though it has not
direct effect on the running of the software for Maneage and the lanugage
environment in Maneage is pre-determined, it is necessary to have it
because if the basic programs see it in the host they will link with it and
will have problems if/when the host's Gettext is updated.
With this commit (which is actually a squashed rebase of 9 commits by Raul
and Mohammad), Gettext and its two extra dependencies (libxml2 and
libunistring) are now installed within Maneage as a basic software and
built before GNU Bash. As a result, all programs built afterwards will
successfully link with our own internal version of Gettext and
libraries. To get this working, some of the basic software dependencies had
to updated and re-ordered and it has been tested in both GNU/Linux and
macoS.
Some other minor issues that are fixed with this commit
- Until this commit, when TeX was not installed, the warning message
saying how to run the configure step in order to re-configure the
project was not showing the option `-e'. However, the use of this option
is more convenient than entering the top-build directory and etc every
time. So with this commit, the warning message has been changed in order
use the option `-e' in the re-configure of the project.
- Until now, on macOS systems, Bash was not linking with our internally
built `libncurses'. With this commit, this has been fixed by setting
`--withcurses=yes' for Bash's configure script.
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Until now there we had manually inserted a `\' before the `_' of sip_tpv
program. However, we also recently added a step in the configure script to
add a `\' before every `_' when writing the final LaTeX macro. This was
because some C compilers (when the host's is used) have an `_' in their
version that we had no control over.
With this commit, the `\' is removed from `sip_tpv' in its build-rule and
we let the backslash be inserted automatically.
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Until now, when you changed the version of a software in an already-built
system, its tarball would be downloaded, but it wouldn't actually
build. The only way would be to force the build by deleting the main target
of that file (under `.local/version-info/TYPE/PROGRAM'). This was because
the tarballs were an order-only prerequisite which was implemented some
time ago based on some theoretical argument that if the tarball dates
changes, the software should not be rebuilt (because we check the
checksum).
However, the problems this causes are more than those it solves: Users may
forget to delete the main target of the program and mistakenly think that
they are using the new version. The fact that all the numbers going into
the paper also contain this number further hides this.
With this commit, tarballs are no longer order-only and any time a version
of a software is updated, it will be automatically built and not cause
confusion and manual intervention by the users. As a result of this change,
I also had to correct the way we find the tarball from the list of
prerequisites.
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Until this commit, the configure step would fail with an error when
compiling libgit2 on a test system. The origin of this bug, on the OS that
was tested, appears to be that in OpenSSL Version 1.1.1a, openssl/ec.h
fails to include openssl/openconf.h. The bug is described in more detail at
https://savannah.nongnu.org/bugs/index.php?58263
With this commit, this is fixed by manually inserting a necessary
components. In particular, `sed` is used to insert a preprocessor
instruction into `openssl/openconf.h`, defining `DEPRECATED_1_2_0(f)`, for
an arbitrary section of code `f`, to include that code rather than exclude
it or warn about it.
This commit is valid provided that openssl remains at a version earlier
than 1.2.0. Starting at version 1.2.0, deprecation warnings should be run
normally. We have thus moved the version of OpenSSL in `versions.conf' to
the section for programs that need to be manually checked for version
updates with a note to remind the user when reaching that version.
Other packages that use OpenSSL may benefit from this commit, not just
libgit2.
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Until now, if GCC couldn't be built for any reason, Maneage would crash and
the user had no way forward. Since GCC is complicated, it may happen and is
frustrating to wait until the bug is fixed. Also, while debugging Maneage,
when we know GCC has no problem, because it takes so long, it discourages
testing.
With this commit, we have re-activated the `--host-cc' option. It was
already defined in the options of `./project', but its affect was nullified
by hard-coding it to zero in the configure script on GNU/Linux systems. So
with this commit that has been removed and the user can use their own C
compiler on a GNU/Linux operating system also.
Furthermore, to inform the user about this option and its usefulness, when
GCC fails to build, a clear warning message is printed, instructing the
user to post the problem as a bug and telling them how to continue building
the project with the `--host-cc' option.
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Similar to the previous commit (e43e3291483699), following a change made
yesterday in the identification of software names from their tarballs, a
few other problematic names are corrected with this commit: `apr-util',
HDF5, TeX Live's installation tarball and `rpcsvc-proto'.
Even though we have visually checked the list of software, other
unidentified similar cases may remain and will be fixed when found in
practice.
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Until Commit 3409a54 (from yesterday), pkg-config was found correctly in
`reproduce/software/make/basic.mk` by searching for `pkg`. However, commit
a21ea20 made an improvement in the regular expression for relating package
names and download filenames, and the string `pkg-config` with the new
regex no longer simplifies to `pkg`. The result of this was that the
basic.mk could not find `pkg-config` in the list of packages, since it was
still listed as `pkg`. This blocked downloading for a system without
pkg-config preloaded.
With this commit (of just a few bytes), the bug is fixed.
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Until now, the sed script for determining URL download rules in the three
software building Makefiles (`basic.mk', `high-level.mk' and `python.mk')
considered package names such as `fftw-3...` and `fftw2-2.1...` to be
identical. As the example above shows, this would make it hard to include
some software that may hav conflicting non-number names.
With this commit, the SED script that is used to separate the version from
the tarball name only matches numbers that are after a dash
(`-'). Therefore considers `fftw-3...` and `fftw-2...` to be identical, but
`fftw-3-...` and `fftw2-2.1...` to be different. As a result of this
change, the `elif' check for some of the other programs like `m4', or
`help2man' was also corrected in all three Makefiles.
While doing this check on all the software, we noticed that `zlib-version'
is being repeated two times in `version.conf' so it was removed. It caused
no complications, because both were the same number, but could lead to bugs
later.
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Until now, throughout Maneage we were using the old name of "Reproducible
Paper Template". But we have finally decided to use Maneage, so to avoid
confusion, the name has been corrected in `README-hacking.md' and also in
the copyright notices.
Note also that in `README-hacking.md', the main Maneage branch is now
called `maneage', and the main Git remote has been changed to
`https://gitlab.com/maneage/project' (this is a new GitLab Group that I
have setup for all Maneage-related projects). In this repository there is
only one `maneage' branch to avoid complications with the `master' branch
of the projects using Maneage later.
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Of the GCC dynamically linked libraries we need to manually add RPATH to
all and for `libstdc++' we also need to tell it to link with
`libiconv'. Until now, the conditional to check for libstdc++ was not
working and thus libiconv wasn't been added to it.
With this commit the conditional has been corrected and is now
working. Also, to help in reading the logs, an echo statement was added
after every call to PatchELF.
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Until now, when a the raw tarball of some software wasn't usable, I would
put it under my own webpage, or `akhlaghi.org/reproduce-software'. That
same address was also used as a backup server. However, now the project has
a proper name: Maneage. So I changed the directory on my own server to
`akhlaghi.org/maneage-software'.
With this commit, this new address has replaced the old one. But to avoid
crashes in projects that haven't yet merged with the main Maneage branch,
the old `reproduce-software' still works (its actually a symbolic link to
the new directory now).
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Until a few commits ago, PatchELF was built statically because it was used
to patch `libstdc++' at the end of the GCC building phase, but PatchELF
also depends on `libstdc++', so it would crash. However, recently when
patching the GCC libraries, we don't directly apply Patchelf to the
library, first we copy it to a temporary place, do the patching, then put
it in its proper place. So the problem above won't happen any more.
With this commit, I am thus removing the static flag from patchelf and
letting it built dynamically all the time. The main problem was that some
systems don't have a static C++ library, so PatchELF couldn't be built
statically. Instead of adding more checks, we just fixed the core
foundation of the problem.
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Until now the software configuration parameters were defined under the
`reproduce/software/config/installation/' directory. This was because the
configuration parameters of analysis software (for example Gnuastro's
configurations) were placed under there too. But this was terribly
confusing, because the run-time options of programs falls under the
"analysis" phase of the project.
With this commit, the Gnuastro configuration files have been moved under
the new `reproduce/analysis/config/gnuastro' directory and the software
configuration files are directly under `reproduce/software/config'. A clean
build was done with this change and it didn't crash, but it may cause
crashes in derived projects, so after merging with Maneage, please
re-configure your project to see if anything has been missed. Please let us
know if there is a problem.
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In the previous commit, I removed the year from the basic installation of
TeXLive packages, but I forgot to correct this in the high-level TeXLive
packages! This is corrected with this commit.
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It is this time of year again: TeXLive has transitioned to its 2020 release
and the year is imprinted into the installation directory of TeXLive. Until
now, we have had to manually change this year and it caused complications
and was very annoying.
With this commit, the explicit year has been removed from TeXLive's
installation and we now simply put a `maneage' instead of the year. I tried
this on another system and it worked nicely. Until the time that we can
fully install LaTeX packages from source tarballs, this is the best thing
we could do for now.
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Elham Saremi recently reported the following errors when building Numpy in
numpy/core/src/npysort/radixsort.c.src: "error: 'for' loop initial
declarations are only allowed in C99 or C11 mode". After some searching, I
found Issue 14147[1] on Numpy's main repository about the same problem. As
described there, apparently Numpy needs C99 compiler, but doesn't check for
it or set it manually (for some strange reason, leaving it to the packagers
to check if they want!!!).
Any way, after a check with Elham, we were able to fix it by adding the
`--std=c99' to CFLAGS of Numpy's build and with this commit, it is now
being implemented in the core Maneage to not cause a problem in any other
project.
[1] https://github.com/numpy/numpy/issues/14147
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Until now, Astropy was instructed to build its own internal copy of the
Expat library. However, with the recent commits before, Maneage now
includes an installation of Expat and Astropy can't keep the two (its
internal version and the project's version) separate, so they conflict and
don't let Astropy get built.
With this commit, the problem is fixed by setting the Expat library as an
explicit dependency of Astropy and asking Astropy to ignore its internal
copy.
While doing this, I recognized that it is much easier and elegant to add
steps in various stages of the `pybuild' function through hooks instead of
variables. So the fifth argument of the `pybuild' function was removed and
now it actually checks if hooks are defined as functions and if so, they
will be called.
The `pyhook_after' function was also implemented in the installation of
`pybind11' (which needed it, given that the 5th argument of `pybuild' was
removed) and after doing a test-build, I noticed that two lines were not
ending with a `\' in `boost' (a dependency of `pybind11').
Commit written originally by Mohammad Akghlaghi
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Until now, the M4 that was built on macOS had internal problems (as
discussed in #1): it would simply print `Abort trap: 6' in the output and
abort. After looking at the build of Homebrew, I noticed that they apply a
patch (correct one line) to fix this problem. To be able to apply that
patch on macOS systems, I had fully open up the build recipe of M4 and
atleast on the testing system, it was built successfully.
Also, after successfully building M4, and thus Autoconf and thus Minizip,
we were able to build XLSX I/O on a macOS and found out that the internal
library's full address wasn't being put in the libraries and
executables. With this commit, we now use macOS's `install_name_tool' to
correct the positions of the two `libxlsxio_*' libraries in all its
executables.
This commit was originally written by Mohammad Akhlaghi
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Until this commit, only the word `Minizip' was written into the Minizip
installation target (without the version number of Minizip). With this
commit, this minor bug has been fixed by using the appropiate Make
variable: `$(minizip-version)'.
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Minizip is a dependency of XLSX I/O and until now, I was just using the
most recent version I found (2.9.2), but XLSX I/O is written for the
Minizip 1.x series, not 2.x. Somehow it didn't cause a crash on my
computer!!! I think XLSX I/O's CMake is instructed to look into system
directories by default when it doesn't find the directories in the given
places. And because I had installed Minizip on my operating system, it
did't complain.
Upon trying the build on their systems, Yahya, Raul and Zahra reported a
failure in the build of XLSX I/O which was due the to the problem above (we
were installing the wrong version of Minizip!).
With this commit, this has been fixed by installing the 1.x series of
Minizip (whish is actually installed within zlib!).
This commit was original done by Mohammad Akhlaghi.
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With this commit, multiples tabs in the definition of MissFITS tarball
have been removed. Now they are white spaces.
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Until this commit, PyYAML was not set as prerequisite of Astropy. This
package is an optional dependency of Astropy for some particular
functions. However, we have already included PyYAML into this project so
it is available. With this commit, PyYAML has been set as a prerequisite
of Astropy.
In addition to this, Html5lib and Beautifulsoup4 have been also added as
prerequsites of Astropy (and removed from Astroquery prerequisites). I
noticed that both of them are optional dependencies of Astropy.
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In the last update of Astropy to version 4.0 they removed some things
that the previous version of Astroquery needs. As a consequence, it is
also necessary to update the Astroquery version to be a ble to run with
the Astropy 4.0. With this commit, the update of Astroquery to it most
recent version (0.4) has been done.
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MissFITS is package for manipulating FITS files.
I added it as my first commit to the project for educational
purposes.
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Until now, like all software on GNU/Linux systems GCC would be built in RAM
(to speed up the build slightly and also not put too much stress on the
HDDs/SSDs). But some systems don't have enough RAM for building GCC and
will complain and crash.
With this commit, we have added a check on the amount of free space in the
`build_tmp' directory (which will be `/dev/shm' on GNU/Linux systems). If
the amount of free space isn't more than 10GB, then GCC won't be built
there and a temporary directory will be built under the `$(BDIR)/software'
directory for it.
This bug was found by Zahra Sharbaf.
This fixes bug #57853.
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XLSX I/O is a very simple and fast program and library for reading and
writing `.xls' and `.xlsx' files (mainly used by Microsoft Excel) to CSV
files. It has two separate executables that can be called for an Excel file
and will output a CSV plain text file that can then be used within the
pipeline with more standard tools.
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Until now we were mistakenly reporting the version of SED instead of
Texinfo.
With this commit, we corrected it!
This was reported by Raul Infante Sainz.
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Until now, we defined `LIBRARY_PATH' to fix the problem of the `ld' linker
of Binutils needing several `*crt*.o' files to run. However, some software
(for example ImageMagick) over-write `LIBRARY_PATH', therefore there is no
other way than to put a link to these necessary files in our local build
directory.
With this commit, we fixed the problem by putting a link to the system's
relevant files in the local library directory. This fixed the problem with
ImageMagick. Later, when we build the GNU C Library in the project, we
should remove this step.
This bug reported by Raul Castellanos Sanchez.
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Until now, the main download script could only check one server for the
given URL. However, ultimately the actual server that a file is downloaded
from is irrelevant for this project: we actually check its
checksum. Especially in the case of software (which are distributed over
many servers), this can usually be very annoying: the servers may not
properly communicate with the running system and even the 10 trials won't
be enough.
With this commit, the download script
`reproduce/analysis/bash/download-multi-try' can take a new optional
argument (a 5th argument). It assumes this argument is a space-separated
list of server(s) to use as backup for the original URL. When downloading
from the original URL fails, it will look into this list and try
downloading the same file from each given server.
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Until now the shell scripts in the software building phase were in the
`reproduce/software/bash' directory. But given our recent change to a
POSIX-only start, the `configure.sh' shell script (which is the main
component of this directory) is no longer written with Bash.
With this commit, to fix that problem, that directory's name has been
changed to `reproduce/software/shell'.
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Until now, the project would first ask for the basic directories, then it
would start testing the compiler. But that was problematic because the
build directory can come from a previous setting (with `./project configure
-e'). Also, it could confuse users to first ask for details, then suddently
tell them that you don't have a working C library! We also need to store
the CPATH variable in the `LOCAL.conf' because in some cases, the compiler
won't work without it.
With this commit, the compiler checking has been moved at the start of the
configure script. Instead of putting the test program in the build
directory, we now make a temporary hidden directory in the source directory
and delete that directory as soon as the tests are done.
In the process, I also noticed that the copyright year of the two hidden
files weren't updated and corrected them.
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Until now, the initial project scripts were primarily tested with GNU
Bash. But Bash is not generally available on all systems (it has many
features beyond POSIX). Because of this, effectively we were imposing the
requirement on the user that they must have Bash installed. We recently
started this with setting the shebang of `project' and
`reproduce/software/bash/configure.sh' to `/bin/sh'. After doing so, Raul
and Gaspar reported an error on their systems.
To fix the problem, I installed Dash (a minimalist POSIX-compliant shell)
on my computer and temporarily set the shebangs to `/bin/dash', ran the
project configuration step and fixed all issues that came up. With this
commit, it can go all the way to building GCC on my system's Dash. After
this stage (when `high-level.mk' is called), there is no problem, because
we have our own version of GNU Bash and that installed version is used.
Probably some more issues still remain and will hopefully be found in the
future.
While doing this, I also noticed the following two minor issues:
- The `./project configure' option `--input-dir' was not recognized
because it was mistakenly checking `--inputdir'. It has been corrected.
- The test C programs now use the `<<EOF' method instead of `echo'.
- In `basic.mk', the extra space between `syspath' and `:=' was removed
(it was an ancient relic!).
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Until now Perl was built after Coreutils, but I recently noticed that
Coreutils actually uses Perl while creating its manpages. So it is now
built before Coreutils.
Also, while testing on an Amazon AWS EC2 server, we noticed that Coreutils
can't build its man page for `md5sum'. The problem was found to be due to
the fact that until now, we weren't actually setting LD_LIBRARY_PATH to our
installed library path in `basic.mk'. Therefore, it would crash because the
server had an older version of OpenSSL than the one that the template's
Coreutils was built with.
In the meantime (while addressing the issues above, because we only had one
thread on the AWS server) I also noticed a few programs that were using a
summarize compilation command (that just prints `CC xxx.c' instead of the
whole command) so I fixed them by adding `V=1'.
This bug was found by Idafen Santana Pérez.
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Until now, the configuration Makefiles (in
`reproduce/software/config/installation' and `reproduce/analysis/config')
had a `.mk' suffix, similar to the workhorse Makefiles. Although they are
indeed Makefiles, but given their nature (to only keep configuration
parameters), it is confusing (especially to early users) for them to also
have a `.mk' (similar to the analysis or software building Makefiles).
To address this issue, with this commit, all the configuration Makefiles
(in those directories) are now given a `.conf' suffix. This is also assumed
for all the files that are loaded.
The configuration (software building) and running of the template have been
checked with this change from scratch, but please report any error that may
not have been noticed.
THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS
FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE
SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES
ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
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GNU Make 4.3 was just announced, so I have updated it here is well. This
was important because until now the installable version was in alpha-mode
(4.2.90), now its a stable version.
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Until now, GCC wouldn't build properly on Debian-based operating systems
because `ld' needed to link with several necessary C library features like
`crti.o' and `crtn.o' (this is an `ld' issue, not GCC). The solution is to
add the directory containing them to `LIBRARY_PATH'. In the previous
commit, I actually searched for these files, but while testing on another
system, I noticed that it can be problematic (other architectures may
exist).
With this commit, we are actually finding the build architecture of the
running GCC (which is the same as the `ld') and using that to fix a fixed
directory to `LIBRARY_PATH'.
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Until now, when find the versions of the TeXLive packages, we would assume
that `cat-date' is always present (because some packages don't have a
version!). However, apparently an update has been made in the TeXLive
Manager (`tlmgr') and `cat-date' is no longer present! As a result, none of
the TeXLive packages were being printed.
With this commit, it now assumes that `revision' is always present for
every package, but it also attempts to read `cat-date' (for backwards
compatability). When `cat-version' isn't present, it will try printing
`revision' and if that is also not present, it will print the date.
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Until this commit, the checking of X11 installation done to ensure that
it is already available in the host system was crashing in macOS
systems. The reason is that the place of the X11 libraries use to be
`/opt/X11/lib' in macOS systems. With this commit, this issue has been
fixed by adding this directory to the LDFLAGS.
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Newer versions of Astropy package has been released. With this commit,
it has been updated. It has been increased from v3.2.1 to v4.0
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In markdown, to specify that part of the text should be shown as code we
need to put it between two `. But in `reproduce/software/make/README.md',
the code parts started with ` and finished in ' (like the file name above).
With this commit, this has been corrected and it will display properly on
web browsers.
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Until this commit, the number `2' was missing in the checksum variable
name of that library. It was `libxml-checksum' but it should be
`libxml2-checksum'. With this commit, this issue has been fixed.
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An extra backslash in the prerequisites of Jeepney Python package was
causing a crash in the installation of that software. With this commit,
this problem has been fixed by removing the backslash.
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OpenMP takes a LONG TIME to build, so to keep things reproducible we are
explicitly disabling OpenMP, if a user needs OpenMP, its trivial to just
add it as a prerequisite of R. The problem is that in some scenarios (based
on other dependencies and when they were built in the build directory),
OpenMP may be present when R is being installed and in other it may not. We
don't want the result to be different between the two builds.
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With this commit, we now have the core R interpretter within the
template. We should later include instructions to install R packages
(possibly in a separate top-level Makefile like Python).
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Until now, while building Perl, the `-Dlddlflags="-shared $$LDFLAGS"'
option was being used for all systems. However, this caused `symbol(s) not
found for architecture x86_64' problems on macOS systems.
With this commit, this configure option is only passed for GNU/Linux
systems. With it, Perl can be built nicely on both GNU/Linux and macOS.
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