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2020-05-01Fixed OpenSSL deprecation bug on some OSs, causing problems in libgit2Boud Roukema-1/+16
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-5/+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.
2020-04-28Better explanation at the end of the configurationMohammad Akhlaghi-4/+8
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.
2020-04-28Astropy will no longer be installed by defaultMohammad Akhlaghi-1/+1
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.
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.
2020-04-27Aborting with informative error when GNU gettext not foundMohammad Akhlaghi-1/+39
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).
2020-04-27Configuration: improved version separation from tarball nameBoud Roukema-27/+36
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.
2020-04-26Configure.sh: build directory checked for ability to modify permissionsPedram Ashofteh Ardakani-11/+81
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
2020-04-20Configuration: current directory printed properly in stdoutMohammad Akhlaghi-9/+9
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).
2020-04-20Maneage instead of Template in README-hacking.md and copyright noticesMohammad Akhlaghi-111/+84
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).
2020-04-17Removed confusing comment in configure.sh, and extra variableMohammad Akhlaghi-12/+2
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.
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-155/+27
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-12/+10
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
2020-04-05Commenting version numbers with an underscore for LaTeXRaul Infante-Sainz-1/+3
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
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-17/+67
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.
2020-04-03CMake updated to version 3.17.0Raul Infante-Sainz-2/+2
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.
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-3/+3
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-1/+28
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/+38
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/+17
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.
2020-02-11Configure script won't crash without Fortran compiler, only a warningMohammad Akhlaghi-27/+46
Until now, when a Fortran compiler didn't exist on the host operating system, the configure script would crash with a warning. But some projects may not need Fortran, so this is just an extra/annoying crash! With this commit, it will still print the warning, but instead of a crash, it will just sleep for some seconds, then continue. Later, when if a software needs Fortran, it's building will crash, but atleast the user was warned. In the future, we should add a step to check on the necessary software and see if Fortran is necessary for the project or not. The project configuration should indeed crash if Fortran is necessary, but we should tell the user that software XXXX needs Fortran so we can't continue without a Fortran compiler. Also, a small sentence ("Project's configuration will continue in XXXX seconds.") was added after all the warnings that won't cause a crash, so user's don't think its a crash.
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.
2020-02-01Make called with -k during software buildingMohammad Akhlaghi-2/+2
Until now, Make was just run ordinarily on the two Makefiles of the software building phase. Therefore when there was a problem with one software while building in parallel, Make would only complete the running rules and stop afterwards. But when other rules don't depened on the crashed rule, its a waste of time to stop the whole thing. With this commit, both calls to Make in the `configure.sh' script are done with the `-k' option (or `--keep-going' in GNU Make). With this option, if a rule crashes, the other rules that don't depend on it will also be run. Generally, anything that doesn't depend on the crashed rule will be done. The `-k' option is a POSIX definition in Make, so it is present in most implemenetations (for the call to `basic.mk').
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-418/+403
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.
2020-01-31Architecture-specific C headers on Debian-based OSs now accountedMohammad Akhlaghi-6/+15
Rencely the building of GCC was allowed on Debian-based systems that have their basic C library in architecture-specific directories, like `/usr/lib/x86_64-linux-gnu'. However, these systems also have their headers in non-standard locations, for example `/usr/include/x86_64-linux-gnu' and this caused a crash on a new Ubuntu system. /usr/include/stdio.h:27:10: fatal error: bits/libc-header-start.h: No such file or directory 27 | #include <bits/libc-header-start.h> | ^~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. The reason it didn't cause problems on other Ubuntus that we tested before was historic: In the old days, we would ask Ubuntu systems to install multilib features to have GCC. Because they had installed those features, this problem didn't show up! But this wasn't mandatory! With this commit, the `CPATH' environment variable is set (similar to how `LIBRARY_PATH' was set) and this fixed the problem on a clean Debian virtual machine. This bug was reported by Sebastian Luna Valero.
2020-01-27Initial scripts compatible with Dash (minimalistic POSIX)Mohammad Akhlaghi-35/+47
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!).
2020-01-23Hashbangs of project and configure.sh set to /bin/shMohammad Akhlaghi-1/+1
Until now, the hashbang of these two shell scripts was set to `/bin/bash', hence assuming that GNU Bash exists on the host system! But this is an extra requirement on the host operating system and these two scripts should be written such that they operate on a POSIX shell (the generic `/bin/sh' which can point to any shell program). With this commit this has been implemented! We may confront some errors as the system is run on other systems, but we should fix such errors and work hard to make these two scripts as POSIX-compatible as possible (runnable on any shell, so as not to force users to install Bash before running the project). This completes Task #15525.
2020-01-23IMPORTANT: Project preparation is now also done with project makeMohammad Akhlaghi-2/+2
Until now, the main commands to run the project were these: `./project configure' (to build the software), `./project prepare' (to possibly arrange input datasets and build special configuration Makefiles) and finally `./project make' to run the project. The main logic behind the "prepare" phase `top-prepare.mk' is to build configuration files that can be fed into the "make" step and optimize its operation. For example when the total number of necessary inputs for the majority of the analysis is not as large as the total number of inputs. With "prepare" (when necessary), you go through the raw inputs, select the ones that are necessary for the rest of the project. The output of `top-prepare.mk' is a configuration file (a Make variable) that keeps the IDs (numbers, names, etc). That configuration file would then be used in the `top-make.mk' to identify the lower level targets and allow optimal project organization and management. But the last two are both part of the analysis, and while they indeed need different calls to Make to be executed, many projects don't actually need a preparation phase: ultimately, its an implementation choice by the project developers and doesn't concern the project users (or the developers when they are running it). To avoid confusing the users, or simply annoying them when a projet doesn't need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk' Makefiles are called with the single `./project make' command and `./project prepare' has been dropped. I noticed this while writing the paper on this system.
2020-01-22Better explanation for missing static C libraryMohammad Akhlaghi-12/+22
Until now, the explanation for a missing static C library didn't actually guide the users to look above and see the error message! So with this commit, I edited it a little to be more clear (and mention to look above). Also, I noticed that on Amazon AWS systems, the static C library is installed as a separate package, so to help the users, I added the necessary command and some better explanation.
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-31/+31
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-3/+3
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.
2020-01-19Corrected typo in last commit (forgetting \ at end of line)Mohammad Akhlaghi-1/+1
In the previous commmit, I had forgot to add a `\' after the newly added `sys_library_path' variable to the `high-level.mk' call.
2020-01-19LIBRARY_PATH is set accordingly based on the hostMohammad Akhlaghi-20/+58
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'.
2020-01-19Better search for static C library at start of configurationMohammad Akhlaghi-108/+75
Until now, to see if a working static C library and `sys/cdefs.h' exist, we were checking absolute locations like `/usr/include/sys/cdefs.h' or `/usr/lib/libc.a' and `/usr/lib64/libc.a'. But this is not robust because on different systems, they can be in different locations. With this commit, we actually use `find' to find the location of `libc.a' and use that to add elements to CPPFLAGS and LDFLAGS. This should fix the problem on systems that have them on non-standard locations.
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.