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2019-09-06Updated versions of several softwareMohammad Akhlaghi-38/+40
New versions of astropy, bash, cmake, curl, findutils, gawk, gcc, ghostscript, git, make, gsl had recently come so they are updated with this commit. About GNU Findutils and GNU Make: I was bootstrapping (building the tarball of) these two separately separately because their standard tarball release had problems on some systems. Both have been updated now so I am no longer using my own webpage as their main URL. A special note about GNU Make. I just noticed that during bootstrapping, GNU Make would use the fixed version string of `4.2.90' for any commit!!! But fortunately they have officially released their 4.2.90 version, so we are safely using their own webpage. The only difference is the compression format. My old bootstrapped build was `tar.lz', but the standard release is `tar.gz'. Also, all the basic programs (installed in `.local/bin') in `basic.mk' are now existance-only dependencies (after a `|'). Because later programs just use them at a very basic level, so there is no need to rebuild everything when Bash gets updated for example.
2019-08-22OpenMPI environment variable used to disable need for OpenSSHMohammad Akhlaghi-2/+6
Until now, OpenMPI would complain about not having `ssh' or `rsh' as a remote shell feature. However, such features should not be necessary in a reproducible scenario and they also have major security issues. With this commit, we are now using OpenMPI's `OMPI_MCA_plm_rsh_agent' environment variable to disable any remote shell dependency for it (as suggested by Boud). Therefore, any dependency for OpenSSH has been removed. But I thought to keep the build instructions incase it may be useful under some un-foreseen scenario. However, to discourage people from building it, a notice was added ontop of the build instructions. This bug was found, tested and solved thanks to Roberto Baena Gallé and Boud Roukema. This fixes bug #56724.
2019-08-22Minor typo corrected in commentsMohammad Akhlaghi-3/+3
Until now we have followed the convention of using space characters before comment lines in recepies, not tabs. This has been corrected in one case.
2019-08-22Adding fpack and funpack in the installation of CFITSIORaul Infante-Sainz-2/+4
Until this commit, `fpack' and `funpack' were not installed by default with the installation of CFITSIO. It is necessary to explicity do a `make fpack' and `make funpack' to have them installed. With this commit, these two programs have been added.
2019-08-22Fixed typo in beautifulsoup4 Python package checksum nameRaul Infante-Sainz-1/+1
Until this commit, the name of the variable for `beautifulsoup4' checksum was wrong, and because of that, it was not able to install it. With this commit, `beautifulsoup-checksum' has been replaced for `beautifulsoup4-checksum' in the `reproduce/software/make/python.mk' Makefile, and the problem has been fixed. This was not noticed previously because this Python package is only installed when some high level programs are requested to be installed. With this commit the version of `imagemagick' program has been also updated because the previous version is not available in the official website anymore.
2019-08-21Using libgit2 implementation of libconv with the option -DUSE_ICONV=OFFRaul Infante-Sainz-1/+5
When trying to install `libgit2' on my macOS system, it complains about not finding `_iconv*' functions! But apparently `libgit2' has its own implementation of `libiconv' that it uses if it can't find `libiconv' on macOS. So, the solution to this problem was to add `-DUSE_ICONV=OFF' to the configuration options of `libgit2'. I reported this issue that now is fixed thanks to the help of Mohammad Akhlaghi.
2019-08-16Libtiff built without JBIG-KIT supportMohammad Akhlaghi-2/+5
Until now, we weren't explicitly telling libtiff to ignore JBIG-KIT. So on some systems, it would try to link withit and would thus fail. With this commit, we have disabled JBIG-KIT support for libtiff. I tried to import it into the template, but it doesn't have use the standard GNU Build system. Maybe later we can add a set of build rules for it, I don't have time now. Also, this problem with libtiff occurred while building Ghostscript. But was fixed after adding this option to libtiff. So libtiff was added as a dependency of Ghostscript. This bug was reported by Sheeraz Ahmad.
2019-08-16OpenSSH privsep-path now set within project's build directoryMohammad Akhlaghi-1/+2
Until now we weren't setting OpenSSH's `privsep-path' configure option. As a result, it would try to use its default (`/var/empty'). Therefore, when the host doesn't have `/var/empty', OpenSSH would crash because of not having permissions to create this directory. With this commit, we are now using OpenSSH's `--with-privsep-path' configure-time option to explicitly use a directory with the project's build directory. This bug was found by Sheeraz Ahmad and Amina Aahil.
2019-08-15WCSLIB 6.4 doesn't need explicit link with CFITSIOMohammad Akhlaghi-15/+3
This was a bug in WCSLIB 6.3 that has been fixed in WCSLIB 6.4. From WCSLIB's changelog: "The rule change to the Fortran makefile in v6.3 to add getwcstab_f.o to the sharable library causes it to depend on CFITSIO to resolve fits_get_wcstab(). Hence backed out of that change.". The actual error was like this: Undefined symbols for architecture x86_64: "_fits_read_wcstab", referenced from: _ftwcst_ in getwcstab_f.o "_gFitsFiles", referenced from: _ftwcst_ in getwcstab_f.o ld: symbol(s) not found for architecture x86_64
2019-08-08libnsl, libtirpc and rpcsvc installed as non-used biber dependenciesMohammad Akhlaghi-6/+43
These three libraries are dependencies of Biber, so we will need them later, but since we don't build biber from source now, we can't control what library it links with. With this commit, we have just added their versions, checksum, download URL and build rule incase they are useful in other software. Later, when we build Biber (and Texlive in general) from source, we'll be able to use these.
2019-08-08Corrected typo when fixing libffi's installation directoryMohammad Akhlaghi-1/+1
In the line where we checked if libffi is installed in `lib/' or `lib64/', there was a typo that lead to an incorrect result: we had forgot to add a `-f' to the second check. This is corrected with this commit.
2019-08-08Gnuastro's build: removing the `make check' stepMohammad Akhlaghi-2/+1
Until now, unlike most other programs, in Gnuastro we would run `make check', but this causes a crash on some systems, because of its BuildProgram test: a linking error because the library isn't installed yet. Which is natural in cases like this (and must be corrected in future Gnuastro releases). With this commit, the checks of Gnuastro have been removed.
2019-08-08Static PatchELF only built when static C library existsMohammad Akhlaghi-7/+10
Until now, when building PatchELF, we would always require that it be done statically. However, some systems don't have a static C library available for linking. This cause a crash in the static building of PatchELF. But a static PatchELF is necessary for correcting RPATH in GCC's outputs. With this commit, in the configure script we check if a static C library is linkable for the compiler. If it isn't then `host_cc' will be set to 1 and GCC won't be built. We also pass the result of this test to `basic.mk' (through `good_static_lib'), so if a static C library isn't available, it builds a dynamically linked PatchELF. This bug was reported by Elham Saremi.
2019-08-06OpenSSH necessary to use OpenMPIMohammad Akhlaghi-2/+13
Until now, OpenMPI was being installed without any dependency. This was fine because it would indeed build. But the moment you tried loading something that depends on it (for example `mpi4py' through `astropy'), you would get an error complaining that SSH isn't present. With this commit, the pipeline now also installs OpenSSH to solve this problem.
2019-08-05WCSLIB needs -lcfitsio on some systemsMohammad Akhlaghi-1/+13
Until now, we were relying on WCSLIB's internal checking and linking with CFITSIO. But on one macOS system (not others that had no problem!), we noticed that it complains with undefined symbol linking errors to CFITSIO libraries. With this commit, as a fast/ugly solution, we are explicity adding `-lcfitsio' to WCSLIB's `LIBS' variable so all binaries are linked with it automatically. We'll be in touch with the WCSLIB author to see if a better solution can be found.
2019-08-05Libffi builds without Java supportMohammad Akhlaghi-1/+2
Until now, we weren't explicitly disabling Java in the build of libffi because there was no Java platform on the systems we tested. But recently Yahya Sefidbakht report a crash in libffi (reported in bug #56716) because of Java not being compiled properly. Unfortunately libffi doesn't have a configure option to disable Java, but it does have an internal macro (`NO_JAVA_RAW_API'). With this commit, we we defined this macro in the `make' step, and it solved the problem. This fixes bug #56716.
2019-08-05Backup repository set to http://akhlaghi.org/reproduce-softwareMohammad Akhlaghi-15/+17
Some of the software tarballs are directly available on their webpage (for example due to build problems on systems, where we had to clone the software and build its tarball ourselves until the next release). Until now, only for these software, these tarballs were hosted on `http://akhlaghi.org/src'. But now, I have moved a clone of the software backup repository (including all its software) to `http://akhlaghi.org/reproduce-software'. To be more clear and have a single place for the backup software, the URL of those software has also been updated in the project source.
2019-08-01Updated version of mpi4py doesn't conflict with OpenMPIMohammad Akhlaghi-12/+3
Until now, in version 3.0.1, mpi4py couldn't be built with the most recent version of OpenMPI. However, after trying the next version (3.0.2), I noticed that it builds successfully without a problem.
2019-08-01Typo in previous commit correctedMohammad Akhlaghi-1/+0
After making the previous commit, I noticed an extra line (redundantly defining a wrong `BASH_ENV') that should have been deleted. It has been corrected.
2019-08-01Bash startup script for every recipeMohammad Akhlaghi-0/+9
Until now the only way to define the environment of the Make recipes was through the exported Make variables (mostly in `initialize.mk' for the analysis steps for example). However, there is only so much you can do with environment variables! In some situations you want slightly more complicated environment control, like setting an alias or running of scripts (things that are commonly done in the `~/.bashrc' file of users to configure their interactive, non-login shells). With this commit, a `reproduce/software/bash/bashrc.sh' has been defined for this job (which is currently empty!). Every major Make step of the project adds this file as the `BASH_ENV' environment variable, so the shell that is created to execute a recipe first executes this file, then the recipe. Each top-level Makefile also defines a `PROJECT_STATUS' environment variable that enables users to limit their envirnoment setup based on the condition it is being setup (in particular in the early phase of `basic.mk', where the user can't make any assumption about the programs and has to write a portable shell script).
2019-07-31GCC: libstdc++ has a link to libiconvMohammad Akhlaghi-0/+1
After adding the libiconv library to the template, the C++ library uses three of its functions (`libiconv', `libiconv_open' and `libiconv_close'). However, it doesn't explicity link with it inside its shared library! I tried by exporting `LIBS=-liconv' before the GCC configure script but it crashed as soon as it went on to the second GCC building stage (because this environment variable was no longer present there). I also tried adding the C++ configure option of `--enable-cstdio' to the GCC configure options (so it doesn't use iconv according to the manual), but it made no change. With this commit, as a brute-force solution, `patchelf --add-needed' is run on the installed `libstdc++.so', so `libiconv.so' is explicitly included inside the `libstdc++' shared library. This bug was found by Roberto Baena Galle while trying to load Matplotlib (which needed the C++ library). This fixes bug #56702.
2019-07-29Checking software tarball checksums before building softwareMohammad Akhlaghi-239/+292
Until now, there was no check on the integrity of the contents of the downloaded/copied software tarballs, we only relied on the tarball name. This could be bad for reproducibility and security, for example on one server the name of a tarball may be the same but with different content. With this commit, the SHA512 checksums of all the software are stored in the newly created `checksums.mk' (similar to how the versions are stored in the `versions.mk'). The resulting variable is then defined for each software and after downloading/copying the file we check to see if the new tarball has the same checksum as the stored value. If it doesn't the script will crash with an error, informing the user of the problem. The only limitation now is a bootstrapping problem: if the host system doesn't already an `sha512sum' executable, we will not do any checksum verification until we install our `sha512sum' (as part of GNU Coreutils). All the tarballs downloaded after GNU Coreutils are built will have their checksums validated. By default almost all GNU/Linux systems will have a usable `sha512sum' (its part of GNU Coreutils after all for a long time: from the Coreutils Changelog file atleast since 2013). This completes task #15347.
2019-07-28Single wrapper instead of old ./configure, Makefile and ./for-groupMohammad Akhlaghi-12/+23
Until now, to work on a project, it was necessary to `./configure' it and build the software. Then we had to run `.local/bin/make' to run the project and do the analysis every time. If the project was a shared project between many users on a large server, it was necessary to call the `./for-group' script. This way of managing the project had a major problem: since the user directly called the lower-level `./configure' or `.local/bin/make' it was not possible to provide high-level control (for example limiting the environment variables). This was especially noticed recently with a bug that was related to environment variables (bug #56682). With this commit, this problem is solved using a single script called `project' in the top directory. To configure and build the project, users can now run these commands: $ ./project configure $ ./project make To work on the project with other users in a group these commands can be used: $ ./project configure --group=GROUPNAME $ ./project make --group=GROUPNAME The old options to both configure and make the project are still valid. Run `./project --help' to see a list. For example: $ ./project configure -e --host-cc $ ./project make -j8 The old `configure' script has been moved to `reproduce/software/bash/configure.sh' and is called by the new `./project' script. The `./project' script now just manages the options, then passes control to the `configure.sh' script. For the "make" step, it also reads the options, then calls Make. So in the lower-level nothing has changed. Only the `./project' script is now the single/direct user interface of the project. On a parallel note: as part of bug #56682, we also found out that on some macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set to blank. This is no problem because RPATH is automatically set in macOS and the executables and libraries contain the absolute address of the libraries they should link with. But having `DYLD_LIBRARY_PATH' can conflict with some low-level system libraries and cause very hard to debug linking errors (like that reported in the bug report). This fixes bug #56682.
2019-07-27DYLD_LIBRARY_PATH also fixed for macOS systemsMohammad Akhlaghi-16/+18
Until now we were only setting the `LD_LIBRARY_PATH' environment variable for GNU/Linux systems. But macOS systems use the `DYLD_LIBRARY_PATH'. With this commit, for better control over the environment, we are also fixing `DYLD_LIBRARY_PATH' in all the places that we are setting the general environment variables.
2019-07-26PatchELF built statically and updatedMohammad Akhlaghi-1/+7
Until now, like all other software, PatchELF would install with dynamic linking. However, PatchELF links with `libstdc++' so on one system, I noticed that PatchELF gives a segmentation fault and corrupts `libstdc++' while correcting its RPATH (after installing GCC). The solution is to build PatchELF statically. With this commit, we force PatchELF to be built statically (it only installs on GNU/Linux systems anyway, so there is no problem with static linking on macOS). This solved the problem on that system. While looking at its documentation, I also noticed that a new version of PatchELF has been released after almost three years, so it has been updated in the template also. This fixes bug #56673.
2019-07-25Updated version of WCSLIB to 6.3, previously 6.2Mohammad Akhlaghi-2/+2
Some bugs have been fixed in the new version of WCSLIB, so it has been updated in the template.
2019-07-24libgit2 updated to version 0.28.2, from 0.26.0Mohammad Akhlaghi-2/+2
More than two releases and bug fixes have been made to libgit2. So we are now using a more recent version in the template.
2019-07-15Minor corrections in configure and high-levelMohammad Akhlaghi-4/+5
Configure script: when `texlive-ready-tlmgr' is not created, it is similar to not having installed TeXLive. A check was added so in this scenario the `./configure' script doesn't crash. high-level.mk: `cairo' and `pixman' are now installed in parallel and with `V=1' (so the full compilation and linking command is printed).
2019-07-08Corrected typo in the installation of libgit2Mohammad Akhlaghi-1/+1
In one of the last few commits, the commands in the recipe of libgit2 was merged with `&&' so it stops if anything fails. But I had forgot to add a `;' at the end of the `install_name_tool' command. This is corrected with this commit.
2019-07-08Rpath in libstdc++ and passing host_cc to high-levelMohammad Akhlaghi-1/+1
Until this commit, the addion of `-liconv' to `CXXFLAGS' in `high-level.mk' dependend on `host_cc', but I had forgot that `host_cc' isn't defined for `high-level.mk'. It is now defined for this Makefile also in the configure script. Also, the Standard C++ library depends on `libgcc_s.so.1', so after building GCC, it was necessary to add Rpath to it.
2019-07-07Minor corrections in high-level programsMohammad Akhlaghi-23/+24
While doing a clean build, several issues were found in the pipeline and corrected. The main issue was that with the recent installation of `libiconv', the GCC standard C++ library depends on `libiconv', so we need to explicity add an `-liconv' to any C++ compilation. The other corrected points are: - The C++ compiler is now explicitly defined in `CXX'. - libgit2 and WCSLIB's recipes weren't using `&&' between statements, so if there was an error, it would still build the target! - The CMake bootstrapping script now builds much faster in parallel.
2019-07-07Texinfo installed as a dependency of M4Mohammad Akhlaghi-7/+18
While testing on a system with no Texinfo, we noticed that M4 depends on Texinfo. To fix this problem, with this commit, it is now included in the pipeline. While doing a clean build, a few minor issues were also found and corrected in the other rules.
2019-07-07FFTW single-precision library builtMohammad Akhlaghi-8/+7
Until now, we were using the `--enable-single' configure-time option of FFTW to build its single-precision library. The reason was that according to the output of `./configure --help', this was equivalent to `--enable-float'. However, the single precision library wasn't being built. As a result, on systems that already had it, SExtractor would use the system's library and on other systems, it would simply not pass the configure step. With this commit, we are now using `--enable-float' which fixes this problem and installs the `libfftw3f*' libraries (showing that it is not equal to `--enable-single'!). Also, some optimization flags were added to hopefully make it faster. This issue was found thanks to Zahra Sharbaf and Hamed Altafi. This fixes bug #56588.
2019-07-07Using fixed TeX Live repositoryMohammad Akhlaghi-2/+14
Until now, we were letting the TeXLive installer use the default CTAN-chosen mirror based on the host. But in many cases, this is not efficient and sometimes those servers don't work. With this commit, we manually set the server to use (`rit.edu'), which is relatively fast and up to date. In this way, until we build TeXLive from source, every user will be using the same CTAN mirror.
2019-07-04Configuring wget without libiconvMohammad Akhlaghi-0/+4
On some Fedora systems, Wget's build conflicts with libiconv. With this commit, we use Wget's `--without-libiconv-prefix' configure option so it will be built without an outside libiconv.
2019-07-04libffi always installed in the lib directoryMohammad Akhlaghi-1/+11
On some Fedora systems, libffi installs under `lib64', not `lib'. As a result, Python's Setuptools can't find it and will not built (complaining about not finding the `_ctypes' module). With this commit, we fix this problem by explicitly putting a copy of libffi's installed libraries within the `lib' directory. This issue was found while testing the pipeline with Elham Saremi and Hamed Altafi.
2019-07-04C and Fortran compiler environment set in high-level.mkMohammad Akhlaghi-0/+2
Until now, we weren't explicitly setting the C and Fortran compiler environment variables (`CC' and `F77'). As a result, if the user's system had already set them, there would be a problem (and the system's compilers would be used). With this commit, we are explicitly setting these two environment variables at the start of `high-level.mk'. This bug was found after a discussion with Elham Saremi.
2019-06-30Removing libiconv before building pkg-configMohammad Akhlaghi-0/+8
An existing `libiconv' can cause a conflict with `pkg-config', this is why `libiconv' depends on `pkg-config'. On a clean build, `pkg-config' is built first. But when we don't have a clean build (and `libiconv' exists) there will be a problem. With this commit, before re-building `pkg-config', we'll remove any possibly existing installation of `libiconv'.
2019-06-29Imported recent correction from Pierre Gajda, no conflictsMohammad Akhlaghi-1/+1
There was only a conflict with `.file-metadata'.
2019-06-29Added citation for TIDES, sorted progs alphabeticallyMohammad Akhlaghi-105/+121
While reviewing Prasenjit's commits, I noticed that we had forgot to add the citation for TIDES, also to make things clear, the program/library build rules are now sorted alphabetically. Finally, I noticed that after building the TiKZ PDF figures, it is crashing (like on Prasenjit's computer). After looking around, I noticed its because we were setting the of the `TEXINPUTS' environment variable to be the installed TeX Live directory (which was ultimately redundant because by default TeX will look into where it was installed). The important thing is just that we remove any possible value the host system has, not to set new directories.
2019-06-28Fixed a conflict with libiconv and pkg-configPierre Gajda-1/+1
Libiconv has to be installed before pkg-config otherwise there would be a compilation error: gconvert.c:61:2: error: #error GNU libiconv not in use but included iconv.h is from libiconv 61 | #error GNU libiconv not in use but included iconv.h is from libiconv
2019-06-28tides library addedPrasenjit Saha-0/+9
TIDES is an ODE integrator with multiple-precision arithmetic.
2019-06-28Corrections to basic buildPrasenjit Saha-1/+2
Several corrections were necessary in the basic build: 1) the version of GCC on some systems includes an `_' which would cause a crash when building the PDF. 2) libcharset had to be manually added to the Git build.
2019-06-28Libiconv built as a dependency of GitMohammad Akhlaghi-15/+22
Prasenjit Saha reported that while building on a macOS, Git complained about not finding `libiconv' functions. Therefore with this commit, `libiconv' is also built as a dependency of Git. Also, since the build of Binutils (and the subsequent GCC) doesn't depend on the exact versions of the other basic software, they are set as existance-only prerequsites (ignoring their timestamps). This is done to avoid re-building when it is not needed.
2019-06-20Removed old comment above Gnuastro's build ruleMohammad Akhlaghi-5/+0
The comment above Gnuastro's build rule is not longer relevant, so it has been removed.
2019-06-14Binutils is built alone, before GCCMohammad Akhlaghi-40/+55
Until now, on GNU/Linux systems, GNU Binutils was built in parallel with other programs. As a result, the moment that the Binutils executables (most importantly `ld') are being installed, if another program is using them, we can have a crash. For some reason, this crash doesn't happen on Fedora or Arch Linux, but on some Debian-based distors, it causes the following crash when we are building Git (which happened to be built while Binuntils is being installed): credential-cache--daemon.o: file not recognized: File format not recognized In a following run of `./configure' (when Binutils has been installed), Git will build and install successfully. To fix this problem, with this commit, all basic programs are now a prerequisite of Binutils and Binutils is the sole prerequisite of GCC (which is the final target of `basic.mk'). Also, the GCC configure options were re-ordered to be easier to read (the `--with-*' options under each other, the `--enable-*' options under each other and so on).
2019-06-13Metastore now has rpathMohammad Akhlaghi-10/+16
Until now we hadn't noticed that Metastore's build doesn't include an `rpath'. As a result I got a crash during a Git commit. With this commit, on GNU/Linux systems, we now add rpath to the installed Metastore executable. During the build, I also cleaned up the Metastore build recipe to be more clear and readable (in particular we only check the user name and group name when metastore is actually built).
2019-06-12Imported recent work on Imfit, minor conflicts fixedMohammad Akhlaghi-10/+97
The recent work by Raul to import Imfit is now merged into the master branch. Only a few minor conflicts came up due to the update with CFITSIO (that Raul also done in parallel on this branch).
2019-06-12Imfit and libcurl: manually adding rpath on GNU/Linux systemsRaul Infante-Sainz-5/+18
While trying to debug the installation of Imfit, we found out that libcurl doesn't have rpath and is thus linking with the host system's libraries. So rpath is now manually added to the build of libcurl. We also found out that Imfit executables don't have rpath, so it was added to them too.
2019-06-10TeXlive: allows for updating itself and removes old version fileMohammad Akhlaghi-0/+9
Until now, TeXlive would only attempt to download/update LaTeX packages, but after some time, it will be necessary for it to update itself. When this happens, it complains about running it with `update --self'. To fix this problem, before installing/updating the LaTeX packages, we will first update tlmgr in any case. Also, we weren't removing the TeXlive package version file before appending the values to it. So it was just repeating the packages every time it was updated. With this commit, it is being removed on every new build. Finally, the version of Git was updated to its most recent version.