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2020-06-02Core software build before using Make to build other softwareMohammad Akhlaghi-1/+2
Until now, Maneage would only build Flock before building everything else using Make (calling 'basic.mk') in parallel. Flock was necessary to avoid parallel downloads during the building of software (which could cause network problems). But after recently trying Maneage on FreeBSD (which is not yet complete, see bug #58465), we noticed that the BSD implemenation of Make couldn't parse 'basic.mk' (in particular, complaining with the 'ifeq' parts) and its shell also had some peculiarities. It was thus decided to also install our own minimalist shell, Make and compressor program before calling 'basic.mk'. In this way, 'basic.mk' can now assume the same GNU Make features that high-level.mk and python.mk assume. The pre-make building of software is now organized in 'reproduce/software/shell/pre-make-build.sh'. Another nice feature of this commit is for macOS users: until now the default macOS Make had problems for parallel building of software, so 'basic.mk' was built in one thread. But now that we can build the core tools with GNU Make on macOS too, it uses all threads. Furthermore, since we now run 'basic.mk' with GNU Make, we can use '.ONESHELL' and don't have to finish every line of a long rule with a backslash to keep variables and such. Generally, the pre-make software are now organized like this: first we build Lzip before anything else: it is downloaded as a simple '.tar' file that is not compressed (only ~400kb). Once Lzip is built, the pre-make phase continues with building GNU Make, Dash (a minimalist shell) and Flock. All of their tarballs are in '.tar.lz'. Maneage then enters 'basic.mk' and the first program it builds is GNU Gzip (itself packaged as '.tar.lz'). Once Gzip is built, we build all the other compression software (all downloaded as '.tar.gz'). Afterwards, any compression standard for other software is fine because we have it. In the process, a bug related to using backup servers was found in 'reproduce/analysis/bash/download-multi-try' for calling outside of 'basic.mk' and removed Bash-specific features. As a result of that bug-fix, because we now have multiple servers for software tarballs, the backup servers now have their own configuration file in 'reproduce/software/config/servers-backup.conf'. This makes it much easier to maintain the backup server list across the multiple places that we need it. Some other minor fixes: - In building Bzip2, we need to specify 'CC' so it doesn't use 'gcc'. - In building Zip, the 'generic_gcc' Make option caused a crash on FreeBSD (which doesn't have GCC). - We are now using 'uname -s' to specify if we are on a Linux kernel or not, if not, we are still using the old 'on_mac_os' variable. - While I was trying to build on FreeBSD, I noticed some further corrections that could help. For example the 'makelink' Make-function now takes a third argument which can be a different name compared to the actual program (used for examle to make a link to '/usr/bin/cc' from 'gcc'. - Until now we didn't know if the host's Make implementation supports placing a '@' at the start of the recipe (to avoid printing the actual commands to standard output). Especially in the tarball download phase, there are many lines that are printed for each download which was really annoying. We already used '@' in 'high-level.mk' and 'python.mk' before, but now that we also know that 'basic.mk' is called with our custom GNU Make, we can use it at the start for a cleaner stdout. - Until now, WCSLIB assumed a Fortran compiler, but when the user is on a system where we can't install GCC (or has activated the '--host-cc' option), it may not be present and the project shouldn't break because of this. So with this commit, when a Fortran compiler isn't present, WCSLIB will be built with the '--disable-fortran' configuration option. This commit (task #15667) was completed with help/checks by Raul Infante-Sainz and Boud Roukema.
2020-05-23New software: Valgrind and PatchBoud Roukema-1/+6
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.
2020-05-22Corrected copyright notices to fit GPL suggested formatMohammad Akhlaghi-9/+4
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
2020-05-08GNU Gettext built as a dependency of BashRaul Infante-Sainz-2/+4
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.
2020-05-01Fixed OpenSSL deprecation bug on some OSs, causing problems in libgit2Boud Roukema-1/+5
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.
2020-04-27Configuration: improved version separation from tarball nameBoud Roukema-2/+2
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.
2020-04-20Maneage instead of Template in README-hacking.md and copyright noticesMohammad Akhlaghi-11/+8
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.
2020-04-17IMPORTANT: software config directly under reproduce/software/configMohammad Akhlaghi-0/+221
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.