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Until this commit, when the user have previous TeX tarball already
present, the project crashed when trying to re-configure, if there was a
newer version of TeX. This is because TeX are updated yearly. With this
commit, this bug has been fixed. Now, during the installation of TeX, it
checks if this problem happens. If this is the case, then it moves the
old tarball, download the new one and install it. If not, it will just
install the already present tarball or crash because of any other
reason. This probem was recurrent, and each time TeX was updated, the
previous tarball had to be removed manually. But now, with this commit,
it is done automatically. The detection and fix of this bug has been
possible with the help of Mohammad Akhlaghi, thanks!
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Publishing a paper on reproducible research without making it easy for
readers to read the references would defeat the point. Of course we have to
make some compromises with some journals' reluctance to shift towards the
free world, but to satisfy scientific ethics, we should at least provide
clickable URLs to the references, preferably to the ArXiv version if
available [1], and also to the DOI, again, preferably to an open-access
version of the URL if available.
I was not able to fully get this done in the .bst file, so there's an
sed/tr hack done to the .bbl file in `reproduce/analysis/make/paper.mk` to
tidy up commas and spaces.
This commit also reverts some of the hacks in the Akhlaghi IAU Symposium
`tex/src/references.tex` entry, to match the improved .bst file,
`tex/src/IEEEtran_openaccess.bst`, provided here with a different name to
the original, in order to satisfy the LaTeX licence.
[1] https://cosmo.torun.pl/blog/arXiv_refs
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David reported this problem, it happened right after importing IEEEtran,
but for some reason, it didn't happen for me.
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When entering the name of the "listings" package, I had forgot to add the
final 's', so it wasn't being installed on a clean system! I didn't have a
problem until now, because it remained from previous builds.
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Following the fact that the DSJ editor decided that this paper doesn't fit
into their scope, we decided to submit it to IEEE's Computing in Science
and Engineering (CiSE). So with this commit the text was re-written to fit
into their style and word-count limitations.
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The paper is no longer using LuaLaTeX, but raw LaTeX (that saves a DVI), it
is so much faster! Initially I had used LuaLaTeX to use special fonts to
resemble the CODATA Data Science Journal, but all that overhead is no
longer necessary. Therefore I also removed the MANY extra LaTeX packages we
were importing. The paper builds and is able to construct one of its images
(the git-branching figure) with only 7 packages beyond the minimal
TeX/LaTeX installation. Also in terms of processing it is so much faster.
The text is just temporary now, and mainly just a place holder. With the
next commit, I'll fill it with proper text.
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A few small conflicts showed up here and there. They are fixed with this
merge.
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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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Until now, at the end of the configuration step, we would tell the user
this: "To change the configuration later, please re-run './project
configure', DO NOT manually edit the relevant files". However, as Boud
suggested in Bug #58243, this is against our principle to encourage users
to modify Maneage.
With this commit, that explanation has been expanded by a few sentences to
tell the users what to change and warn them in case they decide to change
the build-directory.
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Until now Gnuastro and Astropy where installed by default in any clean
build of Maneage. Gnuastro is used to do the demonstration analysis that is
reported in the paper and Astropy was just there to help in testing the
building of the MANY tools it depends on! It (and its dependencies) also
had several papers that helped show software citation.
However, as Boud suggested in task #15619, the burden of installing them
for a new user may be too much and any future changes will cause merge
conflicts. It may also give the impression that Maneage is only/mainly
written for astronomers.
So with this commit, I am removing Astropy as a default target. But we can
only remove Gnuastro after we include an alternative analysis in the
demonstration `delete-me' files. Following Boud's suggestion in that task,
`TARGETS.conf' was also added to the files to be ignored in any future
merge (in the checklist of `README-hacking.mk'). The solution was already
described there, but mainly focused on the deleted `delete-me' files. So
with this commit, I brought out this item as a more prominent item in the
list. Maybe we can later add the analysis done in the Maneage paper (not
yet published).
In terms of testing the software builds, we already have task #15272
(Single target to build all high-level software, for testing) that aims to
have a single configure option to install ALL high-level software and we
can ask people to try if they like and report errors.
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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, we wouldn't explicity check for GNU gettext. If it was present
on the system, we would just add a link to it in Maneage's installation
directory. However, in bug #58248, Boud noticed that Git (a basic software)
actually needs it to complete its installation. Unfortunately we haven't
had the tiem to include a build of Gettext in Maneage. Because it is mostly
available on many systems, it hasn't been reported too commonly, it also
has many dependencies which make it a little time consuming to install.
So with this commit, we actually check for GNU gettext right after checking
the compiler and if its not available an informative error message is
written to inform the user of the problem, along with suggestions on fixing
it (how to install GNU gettext from their package manager).
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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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Recently (in Commit 8eb0892e) the Gnuastro configuration files moved under
"reproduce/analysis/config/gnuastro" directory (before that they were in
`reproduce/software/config/gnuastro)'. But this hadn't been reflected in it
the variable that defines this directory in `initialize.mk'.
With this commit, the address of the Gnuastro configuration files directory
is corrected, allowing Gnuastro programs to operate properly when it is
used.
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Until now, the comment in the file said that setting the `verify-outputs`
variable to `yes` disables the verification. Looking at
`reproduce/analysis/make/verify.mk` shows that the opposite is true.
With this commit, the word `disable` is replaced with `enable` so that the
user is not confused by the conflict between the source code in the other
file and this comment.
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Until now we only checked for the existance and write-ability of the build
directory. But we recently discovered that if the specified build-directory
is in a non-POSIX compatible partition (for example NTFS), permissions
can't be modified and this can cause crashs in some programs (in
particular, while building Perl, see [1]). The thing that makes this
problem hard to identify is that on such partitions, `chmod' will still
return 0 (so it was hard to find).
With this commit, a check has been added after the user specifies the
build-directory. If the proposed build directory is not able to handle
permissions as expected, the configure script will not continue and will
let the user know and will ask them for another directory.
Also, the two printed characters at the start of error messages were
changed to `**' (instead of `--'). When everything is good, we'll use `--'
to tell the user that their given directory will be used as the build
directory. And since there are multiple checks now, the final message to
specify a new build directory is now moved to the end and not repeated in
every check.
[1] https://savannah.nongnu.org/support/?110220
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[Compared to first submission to DSJ last week with 11436 words in raw PDF,
we have decreased the paper by ~1000 words to 10493 :-)]
As with the previous commits, the moment Boud changed the structure of
sentences, I was able to find the redundancies and remove them! This is a
fascinating feature of collaboration I had never felt before: it is so hard
to find redundancies in my own raw text, but even a minor correction by
someone else suddeny breaks my mental memories/barrier on the sentence,
allowing me to be more critical to it!
Anyway, besides such corrections, I fixed a few other things: 1) In the
DSJ's recently published papers, ther is no `~' between "Figure" and its
number. 2) I noticed that in `tex/src/figure-src-inputconf.tex' I was
actually using manually input strings for the filename, checksum and size!
This was contrary to the whole philosophy of Maneage(!), I must have rushed
and forgot! So LaTeX variables are now defined and used.
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Until now, the message that we printed just before starting to build
software didn't actually print the current directory, but only `pwd'. With
this commit, this is fixed (it uses the `currentdir' variable that is
already found before).
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Until now, the message that we printed just before starting to build
software didn't actually print the current directory, but only `pwd'. With
this commit, this is fixed (it uses the `currentdir' variable that is
already found before).
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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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There weren't any conflicts in this merge.
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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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In the previous commit, we remove the `-static' flag from building PatchELF
because it wasn't necessary any more. Howver, the comment for the check
still included it and could be confusing. This is corrected with this
commit. Also, we don't need the `good_static_libc' variable (that was only
defined to pass onto PatchELF). This has also been corrected.
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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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A few minor conflicts came up that were easily fixed.
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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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Since the journal doesn't accept supplementary files during initial
submission, I have put this link on the PDF for the referee and editors to
access if they want.
Also the `tex/img' file was added to the distribution tarball.
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I was using some special Bash feature before to ignore the distribution
directory itself when copying the files, but that had some problems, so I
just used a simple for loop over a `find' command to ignore it. Also, for
now, we don't need BibLaTeX sources in the project (that is primarily for
arXiv), so to help the referee see a more cleaner contents of this
supplement file.
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TeXLive recently transitioned from its 2019 version to its 2020 version
thanks to Elham Saremi's trial of the this project. The fact that
traditionally Maneage installs all TeXLive packages in a per-year directory
is very annoying and required an update in the core Maneage system every
year. So I suddently recognized that we can fix this by setting a different
name for the directory holding the release year. This has been implemented
with this commit.
I have also done this change in the main Maneage branch for other projects
to also benefit from this correction.
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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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The contents until two commits ago when I started to summarize the paper
are now in a new and shorter format: previously the discussion started on
page 25, but now it starts on page 17. It is still a little longer than
8000 words, but not as significantly as before. I will add the discussion
and also try to summarize it futher before submission.
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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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Raul noticed this during the build: I had mistakenly put an extra `&&' at
the start of the line where the line before ended with a `;'.
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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.
When trying to build Manage (the actual project, not this paper) after
applying the commits before there, Raul discovered this problem.
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').
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Until now we would simply return the version numbers as they were written
into the separate files and situations can happen where the version numbers
contain an underscore (`_'). However, this character is a methematical
character in LaTeX, causing LaTeX to complain and abort.
With this commit, a step has been added at the end of the configure script
to convert any possible `_' to `\_'. Once it is commented (a backslash is
put behind it), the underscore will be printed as it is in the final PDF.
This commit was originally written by Mohammad Akhlaghi
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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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Until now we would simply return the version numbers as they were written
into the separate files and situations can happen where the version numbers
contain an underscore (`_'). However, this character is a methematical
character in LaTeX, causing LaTeX to complain and abort.
With this commit, a step has been added at the end of the configure script
to convert any possible `_' to `\_'. Once it is commented (a backslash is
put behind it), the underscore will be printed as it is in the final PDF.
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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.
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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!).
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With this commit, CMake has been updated to its most recent version.
This upgrade has been done because in the installation of XLSX I/O on
macOS laptop, it crashes complaining about C compiler "not able to
compile a simple test program". After a fast search, I found it could be
possible to just use the most recent version of CMake to solve the
problem. But it didn't work. In any case, it is good to have the most
recent version of CMake included.
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A few minor conflicts occurred and were fixed.
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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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