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2020-06-16XLSX I/O properly accounts for local buildMohammad Akhlaghi-2/+2
Until now, when adding the necessary library flags to the build of XLSX I/O, we were effectively over-writing the 'LDFLAGS' variables. So the compiler was effectively not being told where to look for the necessary libraries. With this commit, to fix the problem, we now append the new linking flags to LDFLAGS in XLSX I/O's build, not over-write it.
2020-06-15OpenSSL now built after PerlMohammad Akhlaghi-1/+1
After trying a clean build of Maneage in a Docker image (with a minimal debian:stable-20200607-slim OS), I noticed that the building of OpenSSL is failing because it doesn't find the proper Perl functionality. To fix it, with this commit, Perl is set as a prerequisite of OpenSSL and this fixed the problem.
2020-06-02Core software build before using Make to build other softwareMohammad Akhlaghi-237/+282
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.
2020-05-28Fixed TeXLive crash because of differing local and server versionsRaul Infante-Sainz-3/+80
Until this commit, when the user had a previous TeXLive tarball already present (in their software-tarball directory) compared to the CTAN server, the project crashed in the configure phase. This was because TeXLive is updated yearly and we don't yet install TeXLive from source (currently we use its own package manager, but we plan to fix this in task #15267). With this commit, we fix the problem by checking the cause of the crash during the installation of TeX. If the crash is due to this particular error, we ignore the old tarball and download the new one and install it (the old one is still kept in '.build/software/tarballs', but will get a '-OLD' in its name. This probem was recurrent, and every year that TeXLive is updated, the previous tarball had to be removed manually! But with this commit, this is done automatically. The detection and fix of this bug has been possible with the help of Mohammad Akhlaghi, thanks!
2020-05-25Unified reference to GNU/Linux and free softwareMohammad Akhlaghi-3/+3
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.
2020-05-23New software: Valgrind and PatchBoud Roukema-0/+37
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-52/+92
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
2020-05-08Installing Scamp with the option --enable-plplot=noRaul Infante-Sainz-1/+3
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).
2020-05-08GNU Gettext built as a dependency of BashRaul Infante-Sainz-53/+58
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.
2020-05-06Corrected latex citation of sip_tpv program (no more \ before _)Mohammad Akhlaghi-1/+1
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.
2020-05-06Software are rebuilt automatically with change of versionMohammad Akhlaghi-227/+232
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.
2020-05-01Fixed OpenSSL deprecation bug on some OSs, causing problems in libgit2Boud Roukema-0/+11
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.
2020-04-29Reactivated --host-cc config option to use host C compilerMohammad Akhlaghi-4/+23
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.
2020-04-28Configration bug fixed: other problematic software names from tarballBoud Roukema-5/+4
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.
2020-04-28Configration bug fixed: identify pkg-config from its tarball nameBoud Roukema-1/+1
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.
2020-04-27Configuration: improved version separation from tarball nameBoud Roukema-25/+34
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-66/+48
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.
2020-04-18Properly adding libiconv to the libraries that libstdc++ links withMohammad Akhlaghi-1/+4
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.
2020-04-17Replaced name of directory under akhlaghi.org as backup serverMohammad Akhlaghi-17/+17
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).
2020-04-17Patchelf is now built dynamicallyMohammad Akhlaghi-11/+2
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.
2020-04-17IMPORTANT: software config directly under reproduce/software/configMohammad Akhlaghi-14/+16
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.
2020-04-13Configure (TeXLive): year correction also in high-level packagesMohammad Akhlaghi-1/+1
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.
2020-04-13Configure (TeXLive): Year of distribution no longer in directoryMohammad Akhlaghi-6/+4
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.
2020-04-12Configure (numpy): added --std=c99 to CFLAGS to fix errorMohammad Akhlaghi-0/+1
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
2020-04-06Astropy now depending on the Expat library to fix internal conflictRaul Infante-Sainz-10/+26
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
2020-04-05The build of M4 and XLSX I/O on macOS has been fixedRaul Infante-Sainz-6/+37
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
2020-04-05Including version number of Minizip in its installation targetRaul Infante-Sainz-1/+1
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)'.
2020-04-05Building Minizip 1.x instead of Minizip 2.xRaul Infante-Sainz-15/+62
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.
2020-04-01Removed multiple tabs in MissFITS tarball definitionRaul Infante-Sainz-1/+1
With this commit, multiples tabs in the definition of MissFITS tarball have been removed. Now they are white spaces.
2020-03-20Adding PyYAML, Html5lib, and Beautifulsoup4 as prerequsites of AstropyRaul Infante-Sainz-4/+4
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.
2020-03-17Astroquery updated to version 0.4Raul Infante-Sainz-1/+1
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.
2020-02-24MissFITS is now added to the templateSurena Fatemi-0/+7
MissFITS is package for manipulating FITS files. I added it as my first commit to the project for educational purposes.
2020-02-19Building of GCC now only done when /dev/shm has more than 10GB freeMohammad Akhlaghi-4/+21
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.
2020-02-16XLSX I/O installed with its two dependencies: expat and minizipMohammad Akhlaghi-0/+32
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.
2020-02-13Corrected version of Texinfo when reportingMohammad Akhlaghi-1/+1
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.
2020-02-13Adding a link to the *crt*.o files in the local install directoryMohammad Akhlaghi-1/+16
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.
2020-02-11Using backup server when original download server failsMohammad Akhlaghi-6/+19
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.
2020-02-01IMPORTANT: reproduce/software/bash renamed to reproduce/software/shellMohammad Akhlaghi-6/+6
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'.
2020-01-31Configure step: compiler checks done before basic settingsMohammad Akhlaghi-1/+6
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.
2020-01-27Initial scripts compatible with Dash (minimalistic POSIX)Mohammad Akhlaghi-1/+1
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!).
2020-01-22Perl is now a dependency of Coreutils, LD_LIBRARY_PATH in basic.mkMohammad Akhlaghi-67/+80
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 PĂ©rez.
2020-01-20IMPORTANT!!! Configuration Makefiles now have a .conf suffixMohammad Akhlaghi-12/+12
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.
2020-01-19GNU Make updated to version 4.3Mohammad Akhlaghi-1/+1
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.
2020-01-19LIBRARY_PATH is set accordingly based on the hostMohammad Akhlaghi-4/+18
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'.
2020-01-18TeXLive version printing updated to include revisionMohammad Akhlaghi-7/+26
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.
2020-01-13Adding X11 libraries path to LDFLAGS in Ghostscript installationRaul Infante-Sainz-1/+4
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.
2020-01-13Updated verion of Astropy to 4.0 the most recent oneRaul Infante-Sainz-1/+1
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
2020-01-11Corrected markdown code notations in one README.mdMohammad Akhlaghi-4/+4
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.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-9/+9
Now that its 2020, its necessary to include this year in the copyright statements.
2019-12-18Fixing Libxml2 checksum variable nameRaul Infante-Sainz-1/+1
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.